Review of Medical Microbiology and Immunology, 13th Edition

39. RNA Enveloped Viruses



Influenza Viruses


Measles Virus

Mumps Virus

Respiratory Syncytial Virus

Parainfluenza Viruses




Rubella Virus

Other Togaviruses


Rabies Virus


Human T-Cell Lymphotropic Virus

Self-Assessment Questions

Summaries of Organisms

Practice Questions: USMLE & Course Examinations



Influenza viruses are important human pathogens because they cause both outbreaks of influenza that sicken and kill thousands of people each year as well as infrequent but devastating worldwide epidemics (pandemics).

Influenza viruses are the only members of the orthomyxovirus family. The orthomyxoviruses differ from the paramyxoviruses primarily in that the former have a segmented RNA genome (usually eight pieces), whereas the RNA genome of the latter consists of a single piece.1 The term myxo refers to the observation that these viruses interact with mucins (glycoproteins on the surface of cells).

In addition, the orthomyxoviruses are smaller (110 nm in diameter) than the paramyxoviruses (150 nm in diameter). See Table 39–1 for additional differences.

TABLE 39–1 Properties of Orthomyxoviruses and Paramyxoviruses


Table 39–2 shows a comparison of influenza A virus with several other viruses that infect the respiratory tract. Table 39–3 describes some of the important clinical features of influenza virus and compares them with the clinical features of the other medically important viruses in this chapter.

TABLE 39–2 Features of Viruses That Infect the Respiratory Tract1


TABLE 39–3 Clinical Features of Certain RNA Enveloped Viruses


In 1997, an outbreak of human influenza (avian influenza, bird flu) caused by an H5N1 strain of influenza A virus began. This outbreak and subsequent outbreaks are described on page 308. In 2009, there was an outbreak of human influenza caused by an H1N1 influenza A virus of swine origin (swine-origin influenza virus, S-OIV). This outbreak and the subsequent pandemic are described on page 309. In 2013, an outbreak of influenza caused by an H7N9 strain of influenza virus occurred.

1. Human Influenza Virus


Influenza A virus causes worldwide epidemics (pandemics) of influenza, influenza B virus causes major outbreaks of influenza, and influenza C virus causes mild respiratory tract infections but does not cause outbreaks of influenza. Pandemics occur when a variant of influenza A virus that contains a new hemagglutinin against which people do not have preexisting antibodies is introduced into the human population.

The pandemics caused by influenza A virus occur infrequently (the last one was in 1968), but major outbreaks caused by this virus occur virtually every year in many countries. Each year, influenza is the most common cause of respiratory tract infections that result in physician visits and hospitalizations in the United States.

In the 1918 influenza pandemic, more Americans died than in World War I, World War II, the Korean War, and the Vietnam War combined. Influenza B virus does not cause pandemics, and the major outbreaks caused by this virus do not occur as often as those caused by influenza A virus. It is estimated that approximately 36,000 people die of influenza each year in the United States.

Important Properties

Influenza virus is composed of a segmented single-stranded RNA genome, a helical nucleocapsid, and an outer lipoprotein envelope (Figure 39–1). The virion contains an RNA-dependent RNA polymerase, which transcribes the negative-polarity genome into mRNA.


FIGURE 39–1 Influenza virus—electron micrograph. Long arrow points to the helical nucleocapsid of influenza virus. The nucleocapsid contains the segmented, negative-polarity genome RNA. Short arrow points to the spikes on the virion envelope. The spikes are the hemagglutinin and neuraminidase proteins. (Figure courtesy of Dr. Erskine Palmer and Dr. M. Martin, Public Health Image Library, Centers for Disease Control and Prevention.)

The envelope is covered with two different types of spikes, a hemagglutinin and a neuraminidase.2 Influenza A virus has 16 antigenically distinct types of hemagglutinin and 9 antigenically distinct types of neuraminidase. As discussed later, some of these types cause disease in humans, but most of the types typically cause disease in other animal species such as birds, horses, and pigs.

The function of the hemagglutinin is to bind to the cell surface receptor (neuraminic acid, sialic acid) to initiate infection of the cell. In the clinical laboratory, the hemagglutinin agglutinates red blood cells, which is the basis of a diagnostic test called the hemagglutination inhibition test. The hemagglutinin is also the target of neutralizing antibody (i.e., antibody against the hemagglutinin inhibits infection of the cell).

The neuraminidase cleaves neuraminic acid (sialic acid) to release progeny virus from the infected cell. The hemagglutinin functions at the beginning of infection, whereas the neuraminidase functions at the end. Neuraminidase also degrades the protective layer of mucus in the respiratory tract. This enhances the ability of the virus to gain access to the respiratory epithelial cells.

Influenza viruses, especially influenza A virus, show changes in the antigenicity of their hemagglutinin and neuraminidase proteins; this property contributes to their capacity to cause devastating worldwide epidemics (pandemics). There are two types of antigenic changes: (1) antigenic shift, which is a major change based on the reassortment of segments of the genome RNA; and (2) antigenic drift, which is a minor change based on mutations in the genome RNA. Note that in reassortment, entire segments of RNA are exchanged, each one of which codes for a single protein (e.g., the hemagglutinin) (Figure 39–2).


FIGURE 39–2 Antigenic shift in influenza virus. A human strain of influenza virus containing the gene encoding one antigenic type of hemagglutinin (colored orange) infects the same lung cell as a chicken strain of influenza virus containing the gene encoding a different antigenic type of hemagglutinin (colored black). Reassortment of the genome RNA segments that encode the hemagglutinin occurs, and a new strain of influenza virus is produced containing the chicken type of hemagglutinin (colored black).

Influenza A virus has two matrix proteins: The M1 matrix protein is located between the internal nucleoprotein and the envelope and provides structural integrity. The M2 matrix protein forms an ion channel between the interior of the virus and the external milieu. This ion channel plays an essential role in the uncoating of the virion after it enters the cell. It transports protons into the virion causing the disruption of the envelope, which frees the nucleocapsid containing the genome RNA, allowing it to migrate to the nucleus.

Influenza viruses have both group-specific and type-specific antigens.

(1) The internal ribonucleoprotein is the group-specific antigen that distinguishes influenza A, B, and C viruses.

(2) The hemagglutinin and the neuraminidase are the type-specific antigens located on the surface. Antibody against the hemagglutinin neutralizes the infectivity of the virus (and prevents disease), whereas antibody against the group-specific antigen (which is located internally) does not. Antibody against the neuraminidase does not neutralize infectivity but does reduce disease by decreasing the amount of virus released from the infected cell and thus reducing spread of the virus to adjacent cells.

An important determinant of the virulence of this virus is a nonstructural protein called NS-1 encoded by the genome RNA of influenza virus. NS-1 has several functions, but the one pertinent to virulence is its ability to inhibit the production of interferon mRNA. As a result, innate defenses are reduced and viral virulence is correspondingly enhanced.

Many species of animals (e.g., aquatic birds, chickens, swine, and horses) have their own influenza A viruses. These animal viruses are the source of the RNA segments that encode the antigenic shift variants that cause epidemics among humans. For example, if an avian and a human influenza A virus infect the same cell (e.g., in a farmer’s respiratory tract), reassortment could occur and a new variant of the human A virus, bearing the avian virus hemagglutinin, may appear (Figure 39–1).

There is evidence that aquatic birds (waterfowl) are a common source of these new genes and that the reassortment event leading to new human strains occurs in pigs. In other words, pigs may serve as the “mixing bowl” within which the human, avian, and swine viruses reassort. There are 16 types of hemagglutinin (H1 to H16) and 9 types of neuraminidase (N1 to N9) found in waterfowl. In humans, three types of hemagglutinin (H1, H2, and H3) and two types of neuraminidase (N1 and N2) predominate.

Because influenza B virus is only a human virus, there is no animal source of new RNA segments. Influenza B virus therefore does not undergo antigenic shifts. It does, however, undergo enough antigenic drift that the current strain must be included in the new version of the influenza vaccine produced each year. Influenza B virus has no antigens in common with influenza A virus.

A/Philippines/82 (H3N2) illustrates the nomenclature of influenza viruses. “A” refers to the group antigen. Next are the location and year the virus was isolated. H3N2 is the designation of the hemagglutinin (H) and neuraminidase (N) types. The H1N1 and H3N2 strains of influenza A virus are the most common at this time and are the strains included in the current vaccine. The H2N2 strain caused a pandemic in 1957.

Summary of Replicative Cycle

The virus adsorbs to the cell when the viral hemagglutinin interacts with sialic acid receptors on the cell surface. (The hemagglutinin on the virion surface is cleaved by extracellular proteases to generate a modified hemagglutinin that actually mediates attachment to the cell surface.) The virus then enters the cell in vesicles and uncoats within an endosome. Uncoating is facilitated by the low pH within the endosome. Protons pass through the ion channel formed by the M2 protein into the interior of the virion. This disrupts the virion envelope and frees the nucleocapsid to enter the cytoplasm and then migrate to the nucleus where the genome RNA is transcribed.

The virion RNA polymerase transcribes the eight genome segments into eight mRNAs in the nucleus. Synthesis of the eight mRNAs occurs in the nucleus because a methylated guanosine “cap” is required. The cap is obtained from cellular nuclear RNAs in a process called “cap snatching.” Most of the mRNAs move to the cytoplasm, where they are translated into viral proteins. Some of the viral mRNAs remain in the nucleus, where they serve as the template for the synthesis of the negative-strand RNA genomes for the progeny virions. Replication of the progeny genomes is performed by a different subunit of the viral RNA polymerase (acting as a replicase) from the subunit that functioned earlier as a transcriptase that synthesized the mRNAs. Two newly synthesized proteins, NP protein and matrix protein, bind to the progeny RNA genome in the nucleus, and that complex is transported to the cytoplasm.

The helical ribonucleoprotein assembles in the cytoplasm, matrix protein mediates the interaction of the nucleocapsid with the envelope, and the virion is released from the cell by budding from the outer cell membrane at the site where the hemagglutinin and neuraminidase are located. The neuraminidase releases the virus by cleaving neuraminic acid on the cell surface at the site of the budding progeny virions. Influenza virus, hepatitis delta virus, and retroviruses are the only RNA viruses that have an important stage of their replication take place in the nucleus.

Transmission & Epidemiology

The virus is transmitted by airborne respiratory droplets. The ability of influenza A virus to cause epidemics is dependent on antigenic changes in the hemagglutinin and neuraminidase. As mentioned previously, influenza A virus undergoes both major antigenic shifts as well as minor antigenic drifts. Antigenic shift variants appear infrequently, whereas drift variants appear virtually every year. The last major antigenic shift that caused a pandemic in humans was in 1968 when H3N2 emerged. Epidemics and pandemics (worldwide epidemics) occur when the antigenicity of the virus has changed sufficiently that the preexisting immunity of many people is no longer effective. The antigenicity of influenza B virus undergoes antigenic drift but not antigenic shift. The antigenic changes exhibited by influenza B virus are less dramatic and less frequent than those of influenza A virus.

Influenza occurs primarily in the winter months of December to February in the northern hemisphere, when influenza and bacterial pneumonia secondary to influenza cause a significant number of deaths, especially in older people. The morbidity of influenza in children younger than 2 years is also very high, second only to the morbidity in the elderly. In the southern hemisphere (e.g., in Australia and New Zealand), influenza occurs primarily in the winter months of June through August. In the tropics, influenza occurs year round with little seasonal variation.

Pathogenesis & Immunity

After the virus has been inhaled, the neuraminidase degrades the protective mucus layer, allowing the virus to gain access to the cells of the upper and lower respiratory tract. The infection is limited primarily to this area because the proteases that cleave the hemagglutinin are located in the respiratory tract. Despite systemic symptoms, viremia rarely occurs. The systemic symptoms, such as severe myalgias, are due to cytokines circulating in the blood. There is necrosis of the superficial layers of the respiratory epithelium. Influenza virus pneumonia, which can complicate influenza, is interstitial in location.

Immunity depends mainly on secretory IgA in the respiratory tract. IgG is also produced but is less protective. Cytotoxic T cells also play a protective role.

Clinical Findings

After an incubation period of 24 to 48 hours, fever, myalgias, headache, sore throat, and cough develop suddenly. Severe myalgias (muscle pains) coupled with respiratory tract symptoms are typical of influenza. Vomiting and diarrhea are rare. The symptoms usually resolve spontaneously in 4 to 7 days, but influenzal or bacterial pneumonia may complicate the course. One of the well-known complications of influenza is pneumonia caused by Staphylococcus aureus.

Reyes syndrome, characterized by encephalopathy and liver degeneration, is a rare, life-threatening complication in children following some viral infections, particularly influenza B and chickenpox. Aspirin given to reduce fever in viral infections has been implicated in the pathogenesis of Reye’s syndrome.

Laboratory Diagnosis

Although most diagnoses of influenza are made on clinical grounds, laboratory tests are available. The test most commonly used is an enzyme-linked immunosorbent assay (ELISA) for viral antigen in respiratory secretions such as nasal or throat washings, nasal or throat swabs, or sputum. Several rapid ELISA tests suitable for a physician’s office laboratory are available. Two tests (FLU OIA and QuickVue Influenza Test) are based on detection of viral antigen using monoclonal antibodies, and a third test (ZSTATFLU) is based on detection of viral neuraminidase using a substrate of the enzyme that changes color when cleaved by neuraminidase. The rationale for using the rapid tests is that treatment with the neuraminidase inhibitors should be instituted within 48 hours of the onset of symptoms. Other tests such as direct fluorescent antibody and polymerase chain reaction (PCR) are also used.

Influenza can also be diagnosed by the detection of antibodies in the patient’s serum. A rise in antibody titer of at least four-fold in paired serum samples taken early in the illness and 10 days later is sufficient for diagnosis. Either the hemagglutination inhibition or complement fixation (CF) test can be used to assay the antibody titer. Because the second sample is taken 10 days later, this approach is used to make a retrospective diagnosis, often for epidemiologic purposes.


Oseltamivir (Tamiflu) and zanamivir (Relenza) are used for both the treatment and prevention of influenza. They are members of a class of drugs called neuraminidase inhibitors, which act by inhibiting the release of virus from infected cells. This limits the extent of the infection by reducing the spread of virus from one cell to another. These drugs are effective against both influenza A and B viruses, in contrast to amantadine, which is effective only against influenza A viruses.

In 2009, most isolates of H1N1 influenza virus were resistant to Tamiflu. Most isolates of the novel H1N1 (swine) influenza virus (see later) are susceptible; however, Tamiflu-resistant mutants have emerged. H3N2 strains were still susceptible to Tamiflu. Both H1N1 and H3N2 strains remained susceptible to Relenza. In general, H5N1 strains of influenza virus that cause avian influenza (see later) are sensitive to Tamiflu and Relenza but resistant to amantadine and rimantadine.

Tamiflu is taken orally, whereas Relenza is delivered by inhalant directly into the respiratory tract. Clinical studies showed they reduce the duration of symptoms by 1 to 2 days. They also reduce the amount of virus produced and therefore reduce the chance of spread to others. To be effective as treatment, these drugs must be given within 48 hours of the onset of symptoms.

Amantadine (Symmetrel) is approved for both the treatment and prevention of influenza A. However, 90% of the H3N2 strains in the United States are resistant to amantadine (and rimantadine, see later), and so these drugs are no longer recommended. These drugs block the M2 ion channel, thereby inhibiting uncoating. Resistance is caused primarily by point mutations in the gene for the M2 protein.

Note that amantadine is effective only against influenza A, not against influenza B. Rimantadine (Flumadine), a derivative of amantadine, can also be used for treatment and prevention of influenza A and has fewer side effects than amantadine. It should be emphasized that the vaccine is preferred over these drugs in the prevention of influenza.


The main mode of prevention is the vaccine, which contains both influenza A and B viruses. Prior to 2013, the vaccine was trivalent and contained recent isolates of two A strains (H1N1 and H3N2) and one B strain. In 2013, quadrivalent vaccines containing two A strains and two B strains became available. The vaccine is usually reformulated each year to contain the current antigenic strains.

There are two main types of influenza vaccines available in the United States, a killed vaccine and a live, attenuated vaccine. The vaccine that has been used for many years is a killed vaccine containing purified protein subunits of the virus (hemagglutinin and neuraminidase). The virus is inactivated with formaldehyde and then treated with a lipid solvent that disaggregates the virions. Note that the hemagglutinin is the most important antigen because it elicits neutralizing antibody. This vaccine is typically administered intramuscularly. In 2011, a killed influenza vaccine that can be administered intradermally became available.

The other vaccine is a live, attenuated vaccine containing temperature-sensitive mutants of influenza A and B viruses. These temperature-sensitive mutants can replicate in the cooler (33°C) nasal mucosa where they induce IgA, but not in the warmer (37°C) lower respiratory tract. The live virus in the vaccine therefore immunizes but does not cause disease. This vaccine is administered by spraying into the nose (“nasal mist”). The live vaccine should not be given to pregnant women or to immunocompromised individuals.

Most of the vaccines described above are made in chicken eggs, and anyone who has a significant allergy to egg proteins (e.g., anaphylaxis) should not receive these vaccines. However, in 2012, the U.S. Food and Drug Administration (FDA) approved a killed influenza vaccine (Flucelvax) made in calf kidney cell culture. This vaccine has two advantages: It can be given to those with egg allergy, and it has a short turnaround time, so the latest drift mutant can be used.

Also in 2012, the FDA approved a recombinant vaccine (Flublok) made by inserting the gene encoding the viral hemagglutinin into an insect virus (baculovirus) that is propagated in insect cell culture. This vaccine contains purified hemagglutinin as the immunogen. This vaccine can also be given to those with egg allergy.

Note that the killed vaccine is not a good immunogen, because little IgA is made and the titer of IgG is relatively low. Protection lasts only 6 months. Yearly boosters are recommended and should be given shortly before the flu season (e.g., in October). These boosters also provide an opportunity to immunize against the latest antigenic changes. The vaccine should be given to all persons 6 months and older who do not have a contraindication to receive the vaccine. It is especially important that people with chronic diseases, particularly respiratory and cardiovascular conditions, receive the vaccine. It should also be given to health care personnel who are likely to transmit the virus to those at high risk.

One side effect of the influenza vaccine used in the 1970s containing the swine influenza strain that caused influenza in humans was an increased risk of Guillain-Barré syndrome, which is characterized by an ascending paralysis. Analysis of the side effects of the influenza vaccines in use during the last 10 years has shown no increased risk of Guillain-Barré syndrome.

In addition to the vaccine, influenza can be prevented by using oseltamivir, which is described in the treatment section earlier. Oseltamivir is particularly useful in elderly people who have not been immunized and who may have been exposed. Note that this drug should not be thought of as a substitute for the vaccine. Immunization is the most reliable mode of prevention.

2. Avian Influenza Virus Infection in Humans

H5N1 Influenza Virus

In 1997, the H5N1 strain of influenza A virus that causes avian influenza, primarily in chickens, caused an aggressive form of human influenza with high mortality in Hong Kong. In the winter of 2003–2004, an outbreak of avian influenza caused by H5N1 strain killed thousands of chickens in several Asian countries. Millions of chickens were killed in an effort to stop the spread of the disease. Four hundred eight human cases of H5N1 influenza occurred between 2003 and February 2009, resulting in 254 deaths (a mortality rate of 62%). Note that these 408 people were infected directly from chickens. Both the respiratory secretions and the chicken guano contain infectious virus.

The spread of the H5N1 strain from person to person occurs rarely but remains a major concern because it could increase dramatically if reassortment with the human-adapted strains occurs. In 2005, the H5N1 virus spread from Asia to Siberia and into eastern Europe, where it killed thousands of birds but has not caused human disease. As of this writing (December 2009), there have been no cases of human influenza caused by an H5N1 virus in the United States. However, there have been two cases of human influenza caused by an H7N2 strain of avian influenza virus.

The ability of the H5N1 strain to infect chickens (and other birds) more effectively than humans is due to the presence of a certain type of viral receptor throughout the mucosa of the chicken respiratory tract. In contrast, humans have this type of receptor only in the alveoli, not in the upper respiratory tract. This explains why humans are rarely infected with the H5N1 strain. However, when the exposure is intense, the virus is able to reach the alveoli and causes severe pneumonia.

The virulence of the H5N1 strain is significantly greater than the H1N1 and H3N2 strains that have been causing disease in humans for many years. This is attributed to two features of the H5N1 strain, namely, relative resistance to interferon and increased induction of cytokines, especially tumor necrosis factor. The increase in cytokines is thought to mediate the pathogenesis of the pneumonia and acute respiratory distress syndrome (ARDS) seen in H5N1 infection.

The H5N1 strain is sensitive to the neuraminidase inhibitors, oseltamivir (Tamiflu) and zanamivir (Relenza), but not to amantadine and rimantadine. Tamiflu is the drug of choice for both treatment and prevention. There is no human vaccine available against the H5N1 strain, but there is one available for use in avian species. In 2008, the FDA approved an inactivated vaccine against H5N1 influenza virus, but as of this writing, it is not available to the public. The vaccine is being stockpiled in the National Emergency Reserve.

H7N9 Influenza Virus

In 2013, an outbreak of influenza caused by an H7N9 strain of influenza virus occurred. Prior to this time, the H7N9 strain affected only birds, especially chickens. As of July 2013, 133 people have been diagnosed with influenza caused by this virus, 43 of whom have died (32% mortality rate). Cases have been limited to China and Taiwan. There has been no sustained person-to-person spread.

All of the genes of this virus are of avian origin. It acquired its H7 gene from ducks and its N9 gene from wild birds, and all the other genes are from an influenza strain that infects bramblings, a bird common in Asia and Europe. This H7N9 strain is susceptible to the neuraminidase inhibitors, oseltamivir and zanamivir. There is no vaccine.

3. Swine Influenza Virus Infection in Humans

In April 2009, a novel swine origin strain of influenza A (H1N1) virus (swine-origin influenza virus, S-OIV) caused an outbreak of human influenza, which appeared first in Mexico, then in the United States, followed by spread to 208 countries by December 2009. The Centers for Disease Control and Prevention (CDC) uses the name “novel influenza A (H1N1)” for this virus.

As of December 2009, millions of cases have occurred worldwide. There have been so many cases that most countries have stopped documenting the number of cases. Worldwide there have been 9596 deaths, of which 1445 have occurred in the United States. On June 11, 2009, the World Health Organization (WHO) declared a level 6 pandemic (the highest level alert). By August 2010, the number of cases had declined significantly and the pandemic warning was rescinded. As of this writing in November 2013, the number of cases in the United States and worldwide has significantly declined.

The disease affected primarily young people (60% of cases were 18 years old or younger). Symptoms were in general mild, with the few fatalities occurring in medically compromised patients. There was no outbreak of swine influenza in pigs prior to this human outbreak. Eating pork does not transmit the virus.

S-OIV is a quadruple reassortant: The hemagglutinin, nucleoprotein, and nonstructural protein genes are of North American swine origin, the neuraminidase and matrix protein genes are of Eurasian swine origin, the genes that encode two subunits of the polymerase are of North American avian origin, and the gene that encodes the third subunit of the polymerase is of human H3N2 origin.

A triple reassortant strain circulated in North American swine for several years prior to 2009 but caused human influenza only rarely. In the triple reassortant strain, all five of the genes that are not polymerase genes are of North American swine origin and the polymerase genes have the same origin as the quadruple reassortant. This strain does not have genes of Eurasian swine origin.

The key point is that most people worldwide do not have protective antibodies against the swine hemagglutinin of S-OIV even though they may have antibodies against the seasonal strain of H1N1 virus acquired either by immunization or by exposure to the virus itself. Note also that S-OIV spreads readily from human to human in contrast to the avian H5N1 strain that does not.

A PCR test for the diagnosis of S-OIV infection is available. S-OIV is sensitive to oseltamivir and zanamivir but resistant to amantadine and rimantadine. Both an inactivated and a live, attenuated vaccine against S-OIV became widely available in November 2009.


The paramyxovirus family contains four important human pathogens: measles virus, mumps virus, respiratory syncytial virus, and parainfluenza viruses. They differ from orthomyxoviruses in that their genomes are not segmented, they have a larger diameter, and their surface spikes are different (Table 39–1).

Paramyxoviruses are composed of one piece of single-stranded RNA, a helical nucleocapsid, and an outer lipoprotein envelope. The virion contains an RNA-dependent RNA polymerase, which transcribes the negative-polarity genome into mRNA. The genome is therefore not infectious. The envelope is covered with spikes, which contain hemagglutinin, neuraminidase, or a fusion protein that causes cell fusion and, in some cases, hemolysis (Table 39–4).

TABLE 39–4 Envelope Spikes of Paramyxoviruses




This virus causes measles, a disease characterized by a maculopapular rash. It occurs primarily in childhood. (See “Clinical Findings” section for additional information.)

Important Properties

The genome RNA and nucleocapsid of measles virus are those of a typical paramyxovirus (see earlier). The virion has two types of envelope spikes, one with hemagglutinating activity and the other with cell-fusing and hemolytic activities (Table 39–4). It has a single serotype, and the hemagglutinin is the antigen against which neutralizing antibody is directed. Humans are the natural host.

Summary of Replicative Cycle

After adsorption to the cell surface via its hemagglutinin, the virus penetrates and uncoats and the virion RNA polymerase transcribes the negative-strand genome into mRNA. Multiple mRNAs are synthesized, each of which is translated into the specific viral proteins; no polyprotein analogous to that synthesized by poliovirus is made. The helical nucleocapsid is assembled, the matrix protein mediates the interaction with the envelope, and the virus is released by budding from the cell membrane.

Transmission & Epidemiology

Measles virus is transmitted via respiratory droplets produced by coughing and sneezing both during the prodromal period and for a few days after the rash appears. Measles occurs worldwide, usually in outbreaks every 2 to 3 years, when the number of susceptible children reaches a high level. The WHO estimates there are 30 million cases of measles each year worldwide.

The attack rate is one of the highest of viral diseases; most children contract the clinical disease on exposure. When this virus is introduced into a population that has not experienced measles, such as the inhabitants of the Hawaiian Islands in the 1800s, devastating epidemics occur. In malnourished children, especially those in developing countries, measles is a much more serious disease than in well-nourished children. Vitamin A deficiency is especially important in this regard, and supplementation of this vitamin greatly reduces the severity of measles. Patients with deficient cell-mediated immunity (e.g., AIDS patients) have a severe, life-threatening disease when they contract measles.

Pathogenesis & Immunity

After infecting the cells lining the upper respiratory tract, the virus enters the blood and infects reticuloendothelial cells, where it replicates again. It then spreads via the blood to the skin. The rash is caused primarily by cytotoxic T cells attacking the measles virus–infected vascular endothelial cells in the skin. Antibody-mediated vasculitis may also play a role. Shortly after the rash appears, the virus can no longer be recovered and the patient can no longer spread the virus to others. Multinucleated giant cells, which form as a result of the fusion protein in the spikes, are characteristic of the lesions.

Lifelong immunity occurs in individuals who have had the disease. Although IgG antibody may play a role in neutralizing the virus during the viremic stage, cell-mediated immunity is more important. The importance of cell-mediated immunity is illustrated by the fact that agammaglobulinemic children have a normal course of disease, are subsequently immune, and are protected by immunization. Maternal antibody passes the placenta, and infants are protected during the first 6 months of life.

Infection with measles virus can transiently depress cell-mediated immunity against other intracellular microorganisms, such as Mycobacterium tuberculosis, leading to a loss of purified protein derivative (PPD) skin test reactivity, reactivation of dormant organisms, and clinical disease. The proposed mechanism for this unusual finding is that when measles virus binds to its receptor (called CD46) on the surface of human macrophages, the production of interleukin-12 (IL-12), which is necessary for cell-mediated immunity to occur, is suppressed.

Clinical Findings

After an incubation period of 10 to 14 days, a prodromal phase characterized by fever, conjunctivitis (causing photophobia), running nose, and coughing occurs. Kopliks spots are bright red lesions with a white, central dot that are located on the buccal mucosa and are virtually diagnostic. A few days later, a maculopapular rash appears on the face and proceeds gradually down the body to the lower extremities, including the palms and soles (Figure 39–3). The rash develops a brownish hue several days later.


FIGURE 39–3 Measles—note splotchy “morbilliform” macular-papular rash. (Figure courtesy of Public Health Image Library, Centers for Disease Control and Prevention.)

The complications of measles can be quite severe. Encephalitis occurs at a rate of 1 per 1000 cases of measles. The mortality rate of encephalitis is 10%, and there are permanent sequelae, such as deafness and mental retardation, in 40% of cases. In addition, both primary measles (giant cell) pneumonia and secondary bacterial pneumonia occur. Bacterial otitis media is quite common. Subacute sclerosing panencephalitis (SSPE) is a rare, fatal disease of the central nervous system that occurs several years after measles (see Chapter 44).

Measles in a pregnant woman leads to an increased risk of stillbirth rather than congenital abnormalities. Measles virus infection of the fetus is more severe than rubella virus infection, so the former typically causes fetal death, whereas the latter causes congenital abnormalities.

Atypical measles occurs in some people who were given the killed vaccine and were subsequently infected with measles virus. It is characterized by an atypical rash without Koplik’s spots. Because the killed vaccine has not been used for many years, atypical measles occurs only in adults and is infrequent.

Laboratory Diagnosis

Most diagnoses are made on clinical grounds, but the virus can be isolated in cell culture. A greater than fourfold rise in antibody titer can be used to diagnose difficult cases. PCR assay is also used.


There is no antiviral therapy available.


Prevention rests on immunization with the live, attenuated vaccine. The vaccine is effective and causes few side effects. It is given subcutaneously to children at 15 months of age, usually in combination with rubella and mumps vaccines. The vaccine should not be given to children prior to 15 months of age, because maternal antibody in the child can neutralize the virus and reduce the immune response. Because immunity can wane, a booster dose is recommended. The vaccine contains live virus, so it should not be given to immunocompromised persons or pregnant women. The vaccine has decreased the number of cases of measles greatly in the United States; there were only 138 reported cases of measles in 1997. However, outbreaks still occur among unimmunized individuals (e.g., children in inner cities and in developing countries).

The killed vaccine should not be used. Immune globulin can be used to modify the disease if given to unimmunized individuals early in the incubation period. This is especially necessary if the unimmunized individuals are immunocompromised.



This virus causes mumps, a disease characterized by parotid gland swelling. It occurs primarily in childhood. (See “Clinical Findings” section for a more complete description.)

Important Properties

The genome RNA and nucleocapsid are those of a typical paramyxovirus. The virion has two types of envelope spikes: one with both hemagglutinin and neuraminidase activities and the other with cell-fusing and hemolytic activities (Table 39–4).

The virus has a single serotype. Neutralizing antibody is directed against the hemagglutinin. The internal nucleocapsid protein is the S (soluble) antigen detected in the CF test used for diagnosis. Humans are the natural host.

Summary of Replicative Cycle

Replication is similar to that of measles virus (see page 312).

Transmission & Epidemiology

Mumps virus is transmitted via respiratory droplets. Mumps occurs worldwide, with a peak incidence in the winter. About 30% of children have a subclinical (inapparent) infection, which confers immunity. There were only 683 reported cases of mumps in the United States in 1997—a finding attributed to the widespread use of the vaccine. However, in 2006, a resurgence of mumps occurred, with 6584 cases being recorded despite a high (87%) coverage rate for the vaccine.

Pathogenesis & Immunity

The virus infects the upper respiratory tract and then spreads through the blood to infect the parotid glands, testes, ovaries, pancreas, and, in some cases, meninges. Alternatively, the virus may ascend from the buccal mucosa up Stensen’s duct to the parotid gland.

Lifelong immunity occurs in persons who have had the disease. There is a popular misconception that unilateral mumps can be followed by mumps on the other side. Mumps occurs only once; subsequent cases of parotitis can be caused by other viruses such as parainfluenza viruses, by bacteria, and by duct stones. Maternal antibody passes the placenta and provides protection during the first 6 months of life.

Clinical Findings

After an incubation period of 18 to 21 days, a prodromal stage of fever, malaise, and anorexia is followed by tender swelling of the parotid glands, either unilateral or bilateral. There is a characteristic increase in parotid pain when drinking citrus juices. The disease is typically benign and resolves spontaneously within 1 week.

Two complications are of significance. One is orchitis in postpubertal males, which, if bilateral, can result in sterility. Postpubertal males have a fibrous tunica albuginea, which resists expansion, thereby causing pressure necrosis of the spermatocytes. Unilateral orchitis, although quite painful, does not lead to sterility. The other complication is meningitis, which is usually benign, self-limited, and without sequelae. Mumps virus, Coxsackie virus, and echovirus are the three most frequent causes of viral (aseptic) meningitis. The widespread use of the vaccine in the United States has led to a marked decrease in the incidence of mumps meningitis.

Laboratory Diagnosis

The diagnosis of mumps is usually made clinically, but laboratory tests are available for confirmation. The virus can be isolated in cell culture from saliva, spinal fluid, or urine. PCR assay can also be used. In addition, a fourfold rise in antibody titer in either the hemagglutination inhibition or the CF test is diagnostic. A single CF test that assays both the S and the V (viral) antigens can also be used. Because antibody to S antigen appears early and is shortlived, it indicates current infection. If only V antibody is found, the patient has had mumps in the past.

A mumps skin test based on delayed hypersensitivity can be used to detect previous infection, but serologic tests are preferred. The mumps skin test is widely used to determine whether a patient’s cell-mediated immunity is competent.


There is no antiviral therapy for mumps.


Prevention consists of immunization with the live, attenuated vaccine. The vaccine is effective and long-lasting (at least 10 years) and causes few side effects. Two immunizations are recommended, one at 15 months and a booster dose at 4 to 6 years, usually in combination with measles and rubella vaccines. Because it is a live vaccine, it should not be given to immunocompromised persons or pregnant women. Immune globulin is not useful for preventing or mitigating mumps orchitis.

In the late 1980s, outbreaks of mumps occurred in both immunized and unimmunized people. This led to the recommendation in 1989 that a second course of the MMR (measles, mumps, rubella) vaccine be administered. The incidence of mumps fell, and outbreaks did not occur until 2006, when 6584 cases occurred, primarily in college-age individuals who, surprisingly, had received two doses of the vaccine. Waning immunity after the second dose and immunization with a different genotype from the genotype that caused the outbreak are suggested explanations.



Respiratory syncytial virus (RSV) is the most important cause of pneumonia and bronchiolitis in infants. It is also an important cause of otitis media in children and of pneumonia in the elderly and in patients with chronic cardiopulmonary diseases.

Important Properties

The genome RNA and nucleocapsid are those of a typical paramyxovirus (Table 39–1). Its surface spikes are fusion proteins, not hemagglutinins or neuraminidases (Table 39–4). The fusion protein causes cells to fuse, forming multinucleated giant cells (syncytia), which give rise to the name of the virus.

Humans are the natural hosts of RSV. For many years, RSV was thought to have one serotype; however, two serotypes, designated subgroup A and subgroup B, have been detected by monoclonal antibody tests. Antibody against the fusion protein neutralizes infectivity.

Summary of Replicative Cycle

Replication is similar to that of measles virus (see page 312).

Transmission & Epidemiology

Transmission occurs via respiratory droplets and by direct contact of contaminated hands with the nose or mouth. RSV causes outbreaks of respiratory infections every winter, in contrast to many other “cold” viruses, which reenter the community every few years. It occurs worldwide, and virtually everyone has been infected by the age of 3 years. RSV also causes outbreaks of respiratory infections in hospitalized infants; these outbreaks can be controlled by handwashing and use of gloves, which interrupt transmission by hospital personnel.

Pathogenesis & Immunity

RSV infection in infants is more severe and more often involves the lower respiratory tract than in older children and adults. The infection is localized to the respiratory tract; viremia does not occur.

The severe disease in infants may have an immunopathogenic mechanism. Maternal antibody passed to the infant may react with the virus, form immune complexes, and damage the respiratory tract cells. Trials with a killed vaccine resulted in more severe disease, an unexpected finding that supports such a mechanism.

Most individuals have multiple infections caused by RSV, indicating that immunity is incomplete. The reason for this is unknown, but it is not due to antigenic variation of the virus. IgA respiratory antibody reduces the frequency of RSV infection as a person ages.

Clinical Findings

In infants, RSV is an important cause of lower respiratory tract diseases such as bronchiolitis and pneumonia. RSV is also an important cause of otitis media in young children. In older children and young, healthy adults, RSV causes respiratory tract infections such as the common cold and bronchitis. However, in the elderly (people older than 65 years of age) and in adults with chronic cardiopulmonary diseases, RSV causes severe lower respiratory tract disease, including pneumonia.

Laboratory Diagnosis

An enzyme immunoassay (“rapid antigen test”) that detects the presence of RSV antigens in respiratory secretions is commonly used. The presence of the virus can be detected by immunofluorescence on smears of respiratory epithelium or by isolation in cell culture. The cytopathic effect in cell culture is characterized by the formation of multinucleated giant cells. A fourfold or greater rise in antibody titer is also diagnostic. A reverse transcriptase polymerase chain reaction (RT-PCR) test is also available.


Aerosolized ribavirin (Virazole) is recommended for severely ill hospitalized infants, but there is uncertainty regarding its effectiveness. A combination of ribavirin and hyperimmune globulins against RSV may be more effective.


There is no vaccine. Previous attempts to protect with a killed vaccine resulted in an increase in severity of symptoms. Passive immunization with a monoclonal antibody directed against the fusion protein of RSV (palivizumab, Synagis) can be used for prophylaxis in premature or immunocompromised infants. Hyperimmune globulins (RespiGam) are also available for prophylaxis in these infants and in children with chronic lung disease. Nosocomial outbreaks can be limited by handwashing and use of gloves.



These viruses cause croup (acute laryngotracheobronchitis), laryngitis, bronchiolitis, and pneumonia in children and a disease resembling the common cold in adults.

Important Properties

The genome RNA and nucleocapsid are those of a typical paramyxovirus (Table 39–1). The surface spikes consist of hemagglutinin (H), neuraminidase (N), and fusion (F) proteins (Table 39–4). The fusion protein mediates the formation of multinucleated giant cells. The H and N proteins are on the same spike; the F protein is on a separate spike. Both humans and animals are infected by parainfluenza viruses, but the animal strains do not infect humans. There are four types, which are distinguished by antigenicity, cytopathic effect, and pathogenicity (see later). Antibody to either the H or the F protein neutralizes infectivity.

Summary of Replicative Cycle

Replication is similar to that of measles virus (see page 312).

Transmission & Epidemiology

These viruses are transmitted via respiratory droplets. They cause disease worldwide, primarily in the winter months.

Pathogenesis & Immunity

These viruses cause upper and lower respiratory tract disease without viremia. A large proportion of infections are subclinical. Parainfluenza viruses 1 and 2 are major causes of croup. Parainfluenza virus 3 is the most common parainfluenza virus isolated from children with lower respiratory tract infection in the United States. Parainfluenza virus 4 rarely causes disease, except for the common cold.

Clinical Findings

Parainfluenza viruses are best known as the main cause of croup in children younger than 5 years of age. Croup is characterized by a harsh cough and hoarseness. In addition to croup, these viruses cause a variety of respiratory diseases such as the common cold, pharyngitis, laryngitis, otitis media, bronchitis, and pneumonia.

Laboratory Diagnosis

Most infections are diagnosed clinically. The diagnosis can be made in the laboratory either by isolating the virus in cell culture or by observing a fourfold or greater rise in antibody titer. PCR assay can also be used.

Treatment & Prevention

There is neither antiviral therapy nor a vaccine available.




Coronaviruses are an important cause of the common cold, probably second only to rhinoviruses in frequency. In 2002, a new disease, an atypical pneumonia called severe acute respiratory syndrome (SARS), emerged. In 2012, another severe pneumonia called Middle East respiratory syndrome emerged.

Important Properties

Coronaviruses have a nonsegmented, single-stranded, positive-polarity RNA genome. They are enveloped viruses with a helical nucleocapsid. There is no virion polymerase. In the electron microscope, prominent club-shaped spikes in the form of a corona (halo) can be seen. There are two serotypes called 229E and OC43. The genome sequence of the coronavirus that caused the SARS (CoV-SARS) outbreak is different from that of the existing human strains. The genome sequence of different isolates of CoV-SARS is very similar, so the antigenicity of the virus is likely to be quite stable. The receptor for the SARS coronavirus on the surface of cells is angiotensin-converting enzyme-2.

Summary of Replicative Cycle

The virus adsorbs to cells via its surface spikes (hemagglutinin), after which it enters the cytoplasm, where it is uncoated. The positive-strand genome is translated into two large polypeptides, which are self-cleaved by the virus-encoded protease. Two of these peptides aggregate to form the RNA polymerase that replicates the genome. In addition, mRNAs are synthesized and then translated into the structural proteins. The virus is assembled and obtains its envelope from the endoplasmic reticulum, not from the plasma membrane. Replication occurs in the cytoplasm.

Transmission & Epidemiology

Coronaviruses are transmitted by the respiratory aerosol. Infection occurs worldwide and occurs early in life, as evidenced by finding antibody in more than half of children. Outbreaks occur primarily in the winter on a 2- to 3-year cycle.

SARS originated in China in November 2002 and spread rapidly to other countries. As of this writing, there have been 8300 cases and 785 deaths—a fatality rate of approximately 9%. Human-to-human transmission occurs, and some patients with SARS are thought to be “super-spreaders.” Early in the outbreak, many hospital personnel were affected, but respiratory infection control procedures have greatly reduced the spread within hospitals. There are many animal coronaviruses, and they are suspected of being the source of CoV-SARS. The horseshoe bat appears to be the natural reservoir for CoV-SARS, with the civet cat serving as an intermediate host.

In 2012–2013, a new human coronavirus caused an outbreak of serious, often fatal pneumonia in Saudi Arabia and other countries in the region. The disease is called Middle East respiratory syndrome (MERS), and the virus is called MERS coronavirus (MERS-CoV). Its closest relative is a bat coronavirus, and bats are thought to be the reservoir. Person-to-person transmission is low. Another name for the virus is human coronavirus-EMC (HCoV-EMC).

Pathogenesis & Immunity

Coronavirus infection is typically limited to the mucosal cells of the respiratory tract. Approximately 50% of infections are asymptomatic, and it is unclear what role they play in the spread of infection. Immunity following infection appears to be brief, and reinfection can occur.

Pneumonia caused by SARS coronavirus is characterized by diffuse edema resulting in hypoxia. The binding of the virus to angiotensin-converting enzyme-2 (ACE-2) on the surface of respiratory tract epithelium may contribute to the dysregulation of fluid balance that causes the edema in the alveolar space. MERS-CoV binds to CD-26 on the respiratory mucosa, not to ACE-2.

Clinical Findings

The common cold caused by coronavirus is characterized by coryza (rhinorrhea, runny nose), scratchy sore throat, and low-grade fever. This illness typically lasts several days and has no long-term sequelae. Coronaviruses also cause bronchitis.

SARS is a severe atypical pneumonia characterized by a fever of at least 38°C, nonproductive cough, dyspnea, and hypoxia. Chills, rigors, malaise, and headache commonly occur, but sore throat and rhinorrhea are uncommon. Chest X-ray reveals interstitial “ground-glass” infiltrates that do not cavitate. Leukopenia and thrombocytopenia are seen. The incubation period for SARS ranges from 2 to 10 days, with a mean of 5 days. The clinical findings of MERS are similar to those of SARS.

Laboratory Diagnosis

The diagnosis of the “common cold” is primarily a clinical one. If SARS or MERS is suspected, antibody-based and PCR-based tests can be used.

Treatment & Prevention

There is no antiviral therapy or vaccine available. A combination of ribavirin and steroids has been tried in the treatment of life-threatening cases of SARS, but their efficacy is uncertain.




This virus causes rubella and congenital rubella syndrome. Congenital rubella syndrome is characterized by congenital malformations.

Important Properties

Rubella virus is a member of the togavirus family. It is composed of one piece of single-stranded RNA, an icosahedral nucleocapsid, and a lipoprotein envelope. However, unlike the paramyxoviruses, such as measles and mumps viruses, it has a positive-strand RNA and therefore has no virion polymerase. Its surface spikes contain hemagglutinin. The virus has a single antigenic type. Antibody against hemagglutinin neutralizes infectivity. Humans are the natural host.

Summary of Replicative Cycle

Because knowledge of rubella virus replication is incomplete, the following cycle is based on the replication of other togaviruses. After penetration of the cell and uncoating, the plus-strand RNA genome is translated into several nonstructural and structural proteins. Note the difference between togaviruses and poliovirus, which also has a plus-strand RNA genome but translates its RNA into a single large polyprotein, which is subsequently cleaved. One of the nonstructural rubella proteins is an RNA-dependent RNA polymerase, which replicates the genome first by making a minus-strand template and then, from that, plus-strand progeny. Both replication and assembly occur in the cytoplasm, and the envelope is acquired from the outer membrane as the virion exits the cell.

Transmission & Epidemiology

The virus is transmitted via respiratory droplets and from mother to fetus transplacentally. The disease occurs worldwide. In areas where the vaccine is not used, epidemics occur every 6 to 9 years.

In 2005, the CDC declared rubella eliminated from the United States. The few cases that occurred in the United States were acquired outside and imported into this country. Elimination was made possible by the widespread use of the vaccine. As a result, cytomegalovirus is a much more common cause of congenital malformations in the United States than is rubella virus.

Pathogenesis & Immunity

Initial replication of the virus occurs in the nasopharynx and local lymph nodes. From there it spreads via the blood to the internal organs and skin. The origin of the rash is unclear; it may be due to antigen/antibody–mediated vasculitis.

Natural infection leads to lifelong immunity. Second cases of rubella do not occur; similar rashes are caused by other viruses, such as Coxsackie viruses and echoviruses. Antibody crosses the placenta and protects the newborn.

Clinical Findings


Rubella is a milder, shorter disease than measles. After an incubation period of 14 to 21 days, a brief prodromal period with fever and malaise is followed by a maculopapular rash, which starts on the face and progresses downward to involve the extremities (Figure 39–4). Posterior auricular lymphadenopathy is characteristic. The rash typically lasts 3 days. When rubella occurs in adults, especially women, polyarthritis caused by immune complexes often occurs.


FIGURE 39–4 Rubella—note fine, almost confluent macular-papular rash. (Courtesy of Stephen E. Gellis, MD.)

Congenital Rubella Syndrome

The significance of rubella virus is not as a cause of mild childhood disease but as a teratogen. When a nonimmune pregnant woman is infected during the first trimester, especially the first month, significant congenital malformations can occur as a result of maternal viremia and fetal infection. The increased rate of abnormalities during the early weeks of pregnancy is attributed to the very sensitive organ development that occurs at that time. The malformations are widespread and involve primarily the heart (e.g., patent ductus arteriosus), the eyes (e.g., cataracts), and the brain (e.g., deafness and mental retardation).

In addition, some children infected in utero can continue to excrete rubella virus for months after birth, which is a significant public health hazard because the virus can be transmitted to pregnant women. Some congenital shedders are asymptomatic and without malformations and hence can be diagnosed only if the virus is isolated. Congenitally infected infants also have significant IgM titers and persistent IgG titers long after maternal antibody has disappeared.

Laboratory Diagnosis

Rubella virus can be grown in cell culture, but it produces little cytopathic effect (CPE). It is therefore usually identified by its ability to interfere with echovirus CPE. If rubella virus is present in the patient’s specimen and has grown in the cell culture, no CPE will appear when the culture is superinfected with an echovirus. The diagnosis can also be made by observing a fourfold or greater rise in antibody titer between acute-phase and convalescent-phase sera in the hemagglutination inhibition test or ELISA or by observing the presence of IgM antibody in a single acute-phase serum sample. PCR assay can also be used.

In a pregnant woman exposed to rubella virus, the presence of IgM antibody indicates recent infection, whereas a 1:8 or greater titer of IgG antibody indicates immunity and consequent protection of the fetus. If recent infection has occurred, an amniocentesis can reveal whether there is rubella virus in the amniotic fluid, which indicates definite fetal infection.


There is no antiviral therapy.


Prevention involves immunization with the live, attenuated vaccine. The vaccine is effective and long-lasting (at least 10 years) and causes few side effects, except for transient arthralgias in some women. It is given subcutaneously to children at 15 months of age (usually in combination with measles and mumps vaccine) and to unimmunized young adult women if they are not pregnant and will use contraception for the next 3 months. There is no evidence that the vaccine virus causes malformations. Because it is a live vaccine, it should not be given to immunocompromised patients or to pregnant women.

The vaccine has caused a significant reduction in the incidence of both rubella and congenital rubella syndrome. It induces some respiratory IgA, thereby interrupting the spread of virulent virus by nasal carriage.

Immune serum globulins (IG) can be given to pregnant women in the first trimester who have been exposed to a known case of rubella and for whom termination of the pregnancy is not an option. The main problems with giving IG are that there are instances in which it fails to prevent fetal infection and that it may confuse the interpretation of serologic tests. If termination of the pregnancy is an option, it is recommended to attempt to determine whether the mother and fetus have been infected as described in the preceding “Laboratory Diagnosis” section.

To protect pregnant women from exposure to rubella virus, many hospitals require their personnel to demonstrate immunity, either by serologic testing or by proof of immunization.


Several other medically important togaviruses are described in the chapter on arboviruses (see Chapter 42).




This virus causes rabies, an encephalitis.

Important Properties

Rabies virus is the only medically important member of the rhabdovirus family. It has a single-stranded RNA enclosed within a bullet-shaped capsid surrounded by a lipoprotein envelope. Because the genome RNA has negative polarity, the virion contains an RNA-dependent RNA polymerase. Rabies virus has a single antigenic type. The antigenicity resides in the envelope glycoprotein spikes.

Rabies virus has a broad host range: It can infect all mammals, but only certain mammals are important sources of infection for humans (see later).

Summary of Replicative Cycle

Rabies virus attaches to the acetylcholine receptor on the cell surface. After entry into the cell, the virion RNA polymerase synthesizes five mRNAs that code for viral proteins. After replication of the genome viral RNA by a virus-encoded RNA polymerase, progeny RNA is assembled with virion proteins to form the nucleocapsid, and the envelope is acquired as the virion buds through the cell membrane.

Transmission & Epidemiology

The virus is transmitted by the bite of a rabid animal that manifests aggressive, biting behavior induced by the viral encephalitis. The virus is in the saliva of the rabid animal. In the United States, transmission is usually from the bite of wild animals such as skunks, raccoons, and bats; dogs and cats are frequently immunized and therefore are rarely sources of human infection. In recent years, bats have been the source of most cases of human rabies in the United States. Rodents and rabbits do not transmit rabies.

Human rabies has also occurred in the United States in people who have not been bitten, so-called “nonbite” exposures. The most important example of this type of transmission is exposure to aerosols of bat secretions containing rabies virus. Another rare example is transmission in transplants of corneas taken from patients who died of undiagnosed rabies.

In the United States, fewer than 10 cases of rabies occur each year (mostly imported), whereas in developing countries there are hundreds of cases, mostly due to rabid dogs. In 2007, the United States was declared “canine-rabies free”—the result of the widespread immunization of dogs. Worldwide, approximately 50,000 people die of rabies each year.

The country of origin and the reservoir host of a strain of rabies virus can often be identified by determining the base sequence of the genome RNA. For example, a person developed clinical rabies in the United States, but sequencing of the genome RNA revealed that the virus was the Mexican strain. It was later discovered that the man had been bitten by a dog while in Mexico several months earlier.

Pathogenesis & Immunity

The virus multiplies locally at the bite site, infects the sensory neurons, and moves by axonal transport to the central nervous system. During its transport within the nerve, the virus is sheltered from the immune system and little, if any, immune response occurs. The virus multiplies in the central nervous system and then travels down the peripheral nerves to the salivary glands and other organs. From the salivary glands, it enters the saliva to be transmitted by the bite. There is no viremic stage.

Within the central nervous system, encephalitis develops, with the death of neurons and demyelination. Infected neurons contain an eosinophilic cytoplasmic inclusion called a Negri body, which is important in laboratory diagnosis of rabies (Figure 39–5). Because so few individuals have survived rabies, there is no information regarding immunity to disease upon being bitten again.


FIGURE 39–5 Rabies virus—Negri body. Arrow points to a “Negri body,” an inclusion body in the cytoplasm of an infected neuron. (Figure courtesy of Public Health Image Library, Centers for Disease Control and Prevention.)

Clinical Findings

The incubation period varies, according to the location of the bite, from as short as 2 weeks to 16 weeks or longer. It is shorter when bites are sustained on the head rather than on the leg, because the virus has a shorter distance to travel to reach the central nervous system.

Clinically, the patient exhibits a prodrome of nonspecific symptoms such as fever, anorexia, and changes in sensation at the bite site called paresthesias. After the prodrome, rabies manifests as either of two forms: “furious” (encephalitic) or “dumb” (paralytic). The furious form occurs in about 80% of cases. In the furious form, agitation, delirium, seizures, and hydrophobia occur. Hydrophobia is an aversion to swallowing water because of painful spasm of the pharyngeal muscles. In contrast, in the dumb form, these symptoms do not occur. Rather, the spinal cord is primarily involved, and an ascending paralysis occurs. Death almost invariably occurs following both forms, but with the advent of life support systems, a few individuals have survived.

Laboratory Diagnosis

Rapid diagnosis of rabies infection in the animal is usually made by examination of brain tissue by using either PCR assay, fluorescent antibody to rabies virus, or histologic staining of Negri bodies in the cytoplasm of hippocampal neurons (Figure 39–5). The virus can be isolated from the animal brain by growth in cell culture, but this takes too long to be useful in the decision of whether to give the vaccine.

Rabies in humans can be diagnosed by PCR assay; by fluorescent antibody staining of a biopsy specimen, usually taken from the skin of the neck at the hairline; by isolation of the virus from sources such as saliva, spinal fluid, and brain tissue; or by a rise in titer of antibody to the virus. Negri bodies can be demonstrated in corneal scrapings and in autopsy specimens of the brain.


There is no antiviral therapy for a patient with rabies. Only supportive treatment is available.


In the United States, the rabies vaccine contains inactivated virus grown in human diploid cells. (Vaccine grown in monkey lung cells or chick embryo cells is also available.) In other countries, the duck embryo vaccine or various nerve tissue vaccines are available as well. Duck embryo vaccine has low immunogenicity, and the nerve tissue vaccines can cause an allergic encephalomyelitis as a result of a cross-reaction with human myelin. For these reasons, the human diploid cell vaccine (HDCV) is preferred.

There are two approaches to prevention of rabies in humans: preexposure and postexposure immunization. Preexposure immunization with rabies vaccine should be given to individuals in high-risk groups, such as veterinarians, zookeepers, and travelers to areas of hyperendemic infection (e.g., Peace Corps members). Preexposure immunization consists of three doses given on days 0, 7, and 21 or 28. Booster doses are given as needed to maintain an antibody titer of 1:5.

The rabies vaccine is also used routinely postexposure (i.e., after the person has been exposed to the virus via animal bite). The long incubation period of the disease allows the virus in the vaccine sufficient time to induce protective immunity.

Postexposure immunization involves the use of both the vaccine and human rabies immune globulin (RIG, obtained from hyperimmunized persons) plus immediate cleaning of the wound. This is an example of passive–active immunization. Tetanus immunization should also be considered.

The decision to give postexposure immunization depends on a variety of factors, such as (1) the type of animal (all wild animal attacks demand immunization); (2) whether an attack by a domestic animal was provoked, whether the animal was immunized adequately, and whether the animal is available to be observed; and (3) whether rabies is endemic in the area. The advice of local public health officials should be sought. Hospital personnel exposed to a patient with rabies need not be immunized unless a significant exposure has occurred (e.g., a traumatic wound to the health care worker).

If the decision is to immunize, both HDCV and RIG are recommended. Five doses of HDCV are given (on days 0, 3, 7, 14, and 28), but RIG is given only once with the first dose of HDCV (at a different site). HDCV and RIG are given at different sites to prevent neutralization of the virus in the vaccine by the antibody in the RIG. As much as possible of the RIG is given into the bite site, and the remainder is given intramuscularly. If the animal has been captured, it should be observed for 10 days and euthanized if symptoms develop. The brain of the animal should be examined by immunofluorescence.

The vaccine for immunization of dogs and cats consists of inactivated rabies virus. The first immunization is usually given at 3 months of age, with booster doses given either annually or at 3-year intervals. In the United States, an alternative vaccine used in dogs and cats contains live canarypox virus genetically engineered to contain the gene for the envelope protein of rabies virus.



There are two important human retroviruses: human T-cell lymphotropic virus, which is described here, and human immunodeficiency virus (HIV), which is described in Chapter 45.


Human T-cell lymphotropic virus-1 (HTLV-1) causes two distinctly different diseases: a cancer called adult T-cell leukemia/lymphoma and a neurologic disease called HTLV-associated myelopathy (also known as tropical spastic paraparesis or chronic progressive myelopathy). HTLV-2 also appears to cause these diseases, but the association is less clearly documented. (All information in this section refers to HTLV-1 unless otherwise stated.)

Important Properties

HTLV and HIV are the two medically important members of the retrovirus family. Both are enveloped viruses with reverse transcriptase in the virion and two copies of a single-stranded, positive-polarity RNA genome. However, HTLV does not kill T cells, whereas HIV does. In fact, HTLV does just the opposite; it causes malignant transformation that “immortalizes” the infected T cells and allows them to proliferate in an uncontrolled manner.

The genes in the HTLV genome whose functions have been clearly identified are the three structural genes common to all retroviruses, namely, gag, pol, and env, plus two regulatory genes, tax and rex. In general, HTLV genes and proteins are similar to those of HIV in size and function, but the genes differ in base sequence, and therefore the proteins differ in amino acid sequence (and antigenicity). For example, p24 is the major nucleocapsid protein in both HTLV and HIV, but they differ antigenically. The virions of both HTLV and HIV contain a reverse transcriptase, integrase, and protease. The envelope proteins of HTLV are gp46 and gp21, whereas those of HIV are gp120 and gp41.

The proteins encoded by the tax and rex genes play the same functional roles as those encoded by the HIV regulatory genes, tat and rev. The Tax protein is a transcriptional activator, and the Rex protein governs the processing of viral mRNA and its export from the nucleus to the cytoplasm. Tax protein is required for malignant transformation of T cells.

In contrast to other oncogenic retroviruses, such as Rous sarcoma virus in chickens (see page 350), HTLV does not possess an oncogene in its genome and does not integrate its proviral DNA at a specific site near a cellular oncogene in the T-cell DNA (i.e., it does not cause insertional mutagenesis). Rather, it is the activation of transcription of both cellular and viral mRNA synthesis by the Tax protein that initiates oncogenesis. The Tax protein activates the synthesis of IL-2 (which is T-cell growth factor) and of the IL-2 receptor. IL-2 promotes rapid T-cell growth and eventually malignant transformation of the T cell.

The stability of the genes of HTLV is much greater than that of HIV. As a consequence, HTLV does not show the high degree of variability of the antigenicity of the envelope proteins that occurs in HIV.

Summary of Replicative Cycle

The replication of HTLV is thought to follow a typical retroviral cycle, but specific information has been difficult to obtain because the virus grows poorly in cell culture. HTLV primarily infects CD4-positive T lymphocytes. The cellular receptor for the virus is unknown. Within the cytoplasm, reverse transcriptase synthesizes a DNA copy of the genome, which migrates to the nucleus and integrates into cell DNA. Viral mRNA is made by host cell RNA polymerase, and transcription is upregulated by Tax protein, as mentioned earlier. The Rex protein controls the synthesis of the gag/pol mRNA, the env mRNA, and their subsequent transport to the cytoplasm, where they are translated into structural viral proteins. Full-length RNA destined to become progeny genome RNA is also synthesized and transported to the cytoplasm. The virion nucleocapsid is assembled in the cytoplasm, and budding occurs at the outer cell membrane. Cleavage of precursor polypeptides into functional structural proteins is mediated by the virus-encoded protease.

Transmission & Epidemiology

HTLV is transmitted primarily by intravenous drug use, sexual contact, or breast feeding. Transplacental transmission has been rarely documented. Transmission by blood transfusion has greatly decreased in the United States with the advent of screening donated blood for antibodies to HTLV and discarding those that are positive. Transmission by processed blood products, such as immune serum globulins, has not occurred. Transmission is thought to occur primarily by the transfer of infected cells rather than free, extracellular virus. For example, whole blood, but not plasma, is a major source, and infected lymphocytes in semen are the main source of sexually transmitted virus.

HTLV infection is endemic in certain geographic areas, namely, the Caribbean region including southern Florida, eastern South America, western Africa, and southern Japan. The rate of seropositive adults is as high as 20% in some of these areas, but infection can occur anywhere because infected individuals migrate from these areas of endemic infection. At least half the people in the United States who are infected with HTLV are infected with HTLV-2, usually acquired via intravenous drug use.

Pathogenesis & Immunity

HTLV causes two distinct diseases, each with a different type of pathogenesis. One disease is adult T-cell leukemia/lymphoma (ATL) in which HTLV infection of CD4-positive T lymphocytes induces malignant transformation. As described earlier, HTLV-encoded Tax protein enhances synthesis of IL-2 (T-cell growth factor) and IL-2 receptor, which initiates the uncontrolled growth characteristic of a cancer cell. All the malignant T cells contain the same integrated proviral DNA, indicating that the malignancy is monoclonal (i.e., it arose from a single HTLV-infected cell). HTLV remains latent within the malignant T cells (i.e., HTLV is typically not produced by the malignant cells).

The other disease is HTLV-associated myelopathy (HAM), also known as tropical spastic paraparesis or chronic progressive myelopathy. HAM is a demyelinating disease of the brain and spinal cord, especially of the motor neurons in the spinal cord. HAM is caused either by an autoimmune cross-reaction in which the immune response against HTLV damages the neurons or by cytotoxic T cells that kill HTLV-infected neurons.

Clinical Findings

ATL is characterized by lymphadenopathy, hepatosplenomegaly, lytic bone lesions, and skin lesions. These features are caused by proliferating T cells infiltrating these organs. In the blood, the malignant T cells have a distinct “flower-shaped” nucleus. Hypercalcemia due to increased osteoclast activity within the bone lesions is seen. Patients with ATL often have reduced cell-mediated immunity, and opportunistic infections with fungi and viruses are common.

The clinical features of HAM include gait disturbance, weakness of the lower limbs, and low back pain. Loss of bowel and bladder control may occur. Loss of motor function is much greater than sensory loss. T cells with a “flower-shaped” nucleus can be found in the spinal fluid. Magnetic resonance imaging of the brain shows nonspecific findings. Progression of symptoms occurs slowly over a period of years. HAM occurs primarily in women of middle age. The disease resembles multiple sclerosis except that HAM does not exhibit the remissions characteristic of multiple sclerosis.

Both ATL and HAM are relatively rare diseases. The vast majority of people infected with HTLV develop asymptomatic infections, usually detected by the presence of antibody. Only a small subset of those infected develop either ATL or HAM.

Laboratory Diagnosis

Infection with HTLV is determined by detecting antibodies against the virus in the patient’s serum using the ELISA test. The Western blot assay is used to confirm a positive ELISA result. PCR assay can detect the presence of HTLV RNA or DNA within infected cells. The laboratory tests used to screen donated blood contain only HTLV-1 antigens, but because there is cross-reactivity between HTLV-1 and HTLV-2, the presence of antibodies against both viruses is usually detected. However, some HTLV-2 antibodies are missed in these routine screening tests. Isolation of HTLV in cell culture from the patient’s specimens is not done.

ATL is diagnosed by finding malignant T cells in the lesions. The diagnosis of HAM is supported by the presence of HTLV antibody in the spinal fluid or finding HTLV nucleic acids in cells in the spinal fluid.

Treatment & Prevention

There is no specific antiviral treatment for HTLV infection, and no antiviral drug will cure latent infections by HTLV. ATL is treated with anticancer chemotherapy regimens. Antiviral drugs have not been effective in the treatment of HAM. Corticosteroids and danazol have produced improvement in some patients.

There is no vaccine against HTLV. Preventive measures include screening donated blood for the presence of antibodies, using condoms to prevent sexual transmission, and encouraging women with HTLV antibodies to refrain from breast feeding.


1. Regarding influenza virus, which one of the following statements is most accurate?

(A) The virion contains an RNA-dependent DNA polymerase.

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

(C) The protein that undergoes antigenic variation most often is the internal ribonucleoprotein.

(D) Antigenic drift involves major changes in antigenicity that result from reassortment of the segments of its RNA genome.

(E) The neuraminidase on the virion surface mediates the interaction of the virus with the receptors on the respiratory tract epithelium.

2. Regarding influenza virus and the disease influenza, which one of the following statements is most accurate?

(A) Both the killed and the live, attenuated vaccines induce lifelong immunity.

(B) Influenza A virus causes more severe disease and more widespread epidemics than does influenza B virus.

(C) The genome of influenza A virus has eight segments, but the genome of influenza B virus is in one piece.

(D) The classification of influenza viruses into A, B, and C viruses is based on antigenic differences in their hemagglutinin.

(E) Chronic carriers (i.e., patients from whom influenza virus is isolated at least 6 months after the acute disease) are an important source of human infection.

3. Regarding measles virus and the disease measles, which one of the following statements is most accurate?

(A) The measles vaccine contains killed virus as the immunogen.

(B) One of the main sequelae of measles is autoimmune glomerulonephritis and kidney failure.

(C) Measles is unlikely to be eradicated because there is a significant animal reservoir for this virus.

(D) Fecal–oral transmission during the diaper stage is the main mode of acquisition of measles virus.

(E) This virus has only one antigenic type, and lifelong immunity occurs in patients who have had measles.

4. Regarding respiratory syncytial virus (RSV), which one of the following statements is most accurate?

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

(B) RSV causes tumors in newborn animals but not in humans.

(C) The RSV vaccine is recommended for all children prior to entering school.

(D) Amantadine should be given to elderly nursing home residents to prevent outbreaks of disease caused by RSV.

(E) RSV forms intranuclear inclusion bodies within neutrophils that are important in diagnosis by the clinical laboratory.

5. Regarding rubella virus, which one of the following statements is most accurate?

(A) Systemic infection with rubella virus often causes severe liver damage resulting in cirrhosis.

(B) If a pregnant woman is infected during the first trimester, significant fetal abnormalities typically result.

(C) The main source of virus is adults who have recovered from the disease but are chronic carriers of the virus.

(D) Immunization of both male and female health care workers with the formalin-inactivated vaccine is recommended.

(E) The significant changes in the antigenicity of this virus are attributed to reassortment of the segments of its genome.

6. Regarding rabies virus and the disease rabies, which one of the following statements is most accurate?

(A) Finding intranuclear inclusion bodies within macrophages is presumptive evidence of rabies virus infection.

(B) Lamivudine is used to treat rabies because it inhibits the RNA-dependent DNA polymerase in the virion.

(C) In the United States, skunks and bats are more likely to transmit rabies virus to people than are dogs and cats.

(D) The incubation period of the disease is usually 2 to 4 days, leading to the rapid progression of the encephalitis and death.

(E) After the animal bite, rabies virus enters the bloodstream, replicates in internal organs such as the liver, and then reaches the central nervous system during the secondary viremia.

7. A woman was hiking in an isolated area when a skunk appeared and bit her on the leg. She now presents to your emergency room about an hour after the bite. Which one of the following is the most appropriate thing to do?

(A) Give rabies vaccine and hyperimmune globulin immediately.

(B) Reassure her that rabies is not a problem because skunks do not carry rabies.

(C) Quarantine the animal for 10 days and only treat her if signs of rabies appear in the animal.

(D) Test the patient’s serum for antibodies now and in 10 days to see if there is a rise in antibody titer before treating her.

8. Human T-cell lymphotropic virus (HTLV) causes T-cell leukemia in adults. Regarding this virus, which one of the following statements is most accurate?

(A) HTLV is transmitted primarily by the fecal–oral route.

(B) Oseltamivir cures the latent state established by HTLV within T cells.

(C) The genome of HTLV consists of double-stranded RNA; therefore, there is no polymerase in the virion.

(D) HTLV is associated with leukemia in Japan, but the virus has not appeared in the United States at the present time.

(E) Oncogenesis by HTLV is related to a viral transcription factor that activates the production of interleukin-2 and its receptor.

9. Your patient is a 75-year-old woman with fever, chills, and myalgias that began yesterday. It is January and an outbreak of influenza is occurring in the retirement community in which she lives. A rapid test for influenza antigen is positive. Which one of the following is the best choice of drug to treat the infection?

(A) Acyclovir

(B) Amantadine

(C) Interferon

(D) Oseltamivir

(E) Ribavirin


1. (B)

2. (B)

3. (E)

4. (A)

5. (B)

6. (C)

7. (A)

8. (E)

9. (D)


Brief summaries of the organisms described in this chapter begin on page 648. Please consult these summaries for a rapid review of the essential material.


Questions on the topics discussed in this chapter can be found in the Clinical Virology section of PART XIII: USMLE (National Board) Practice Questions starting on page 703. Also see PART XIV: USMLE (National Board) Practice Examination starting on page 731.

1The total molecular weight of influenza virus RNA is approximately (2–4) × 106, whereas the molecular weight of paramyxovirus RNA is higher, approximately (5–8) × 106.

2Paramyxoviruses also have a hemagglutinin and a neuraminidase, but the two proteins are located on the same spike.