Chapter 38: Respiratory Viruses

The viruses described in this chapter are the “professional” respiratory tract viruses whose primary clinical manifestations are in the upper and/or lower respiratory tract (Table 38–1). Many other viruses, such as measles virus, mumps virus, rubella virus, and varicella-zoster virus, initially infect the respiratory tract, but their characteristic clinical findings are seen elsewhere. These viruses are described in other chapters.

Almost all of the respiratory tract viruses have RNA as their genome; one has DNA. Most are enveloped viruses, whereas two, rhinovirus and adenovirus, are nonenveloped. In addition, the enveloped respiratory viruses belong to several different virus families, namely, orthomyxoviruses, paramyxoviruses, and coronaviruses. So they are quite varied in their structure and replication. The feature that unites all of these viruses is their ability to infect the mucosal cells of the respiratory tract and cause significant symptoms there.

In serious respiratory virus infections, a laboratory diagnosis can be made by using polymerase chain reaction (PCR)-based assays on respiratory tract secretions. A panel of PCR assays is used to diagnose infections caused by viruses such as influenza virus, parainfluenza virus, respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus (HMPV), and adenovirus.

Additional information regarding the clinical aspects of infections caused by the viruses in this chapter is provided in Part IX entitled Infectious Diseases beginning on page 607.

Influenza virus is an important human pathogen because it causes both outbreaks of influenza that sicken and kill thousands of people each year as well as infrequent but devastating worldwide epidemics (pandemics).

Influenza virus is the only member 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. The term myxo refers to the observation that these viruses interact with mucins (glycoproteins on the surface of cells). Table 38–2 shows a comparison of the properties of influenza A virus with several other viruses that infect the respiratory tract.

Most cases of influenza in humans are caused by H1N1 and H3N2 strains of influenza A virus (see Summary of Replicative Cycle). However, 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 311. In 2009, there was an outbreak of human influenza caused by H1N1 influenza A virus of swine origin (swine-origin influenza virus, S-OIV). This outbreak and the subsequent pandemic are described on page 312. In 2013, an outbreak of human influenza caused by another bird-related strain (H7N9) of influenza virus occurred.

1. Human Influenza Virus

Disease

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 38–1). The virion contains an RNA-dependent RNA polymerase, which transcribes the negative-polarity genome into mRNA.

The envelope is covered with two different types of spikes, a hemagglutinin and a neuraminidase. 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 38–2).

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 in the nucleocapsid 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 and to block the action of interferon by inhibiting the protein kinase and ribonuclease that mediate interferon’s antiviral action. 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 (see Figure 38–2).

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 is cleaved by cellular proteases to reveal a fusion protein that mediates fusion with the cell membrane. (Note similarity to the Coronavirus entry process described later in this chapter.)

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 (methyl-guanosine plus approximately 10 adjacent nucleotides) is obtained from cellular mRNAs in a process called “cap snatching.” (See Figure 29–4.) The cap serves as the primer for the viral polymerase to synthesize viral mRNA. The capped viral mRNAs then move to the cytoplasm, where they are translated into viral proteins.

In addition, also in the nucleus, full-length positive strand viral RNA transcripts (lacking methyl-guanosine cap and poly-adenosine tail) serve as the template for the synthesis of the negative-strand RNA genomes for the progeny virions.

The polymerase of influenza virus consists of three subunits: the PA subunit is the endonucleases (ribonuclease) that mediates cap-snatching, the PB1 subunit is an RNA polymerase that synthesizes viral mRNAs and progeny genome RNAs, and the PB2 subunit binds capped cellular mRNAs prior to the transfer of the cap by PA that initiates synthesis of viral mRNA (see Figure 29–4). Each of the three subunits is encoded by a separate gene segment and one polymerase heterotrimer (PA, PB1, and PB2) is attached to each gene segment.

Two newly synthesized proteins, NP protein and matrix protein, bind to the progeny RNA genome segments 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 occurring 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.

Although the emphasis is placed on the striking ability of the virus to cause pandemics, it should be noted that influenza A virus causes up to half a million deaths worldwide annually, 90% of which occur in older adults.

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

Influenza virus infection causes inflammation of the mucosa of upper respiratory tract sites such as the nose and pharynx, and lower respiratory tract sites such as the larynx, trachea, and bronchi. Pneumonia, which involves the alveoli, may also occur.

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 either Staphylococcus aureus or Streptococcus pneumoniae.

Reye’s 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. PCR-based tests that detect influenza virus RNA in respiratory specimens are commonly used in hospitals. Nucleic acid amplification tests (NAAT) have high specificity and acceptably specificity. These tests will diagnose infections caused by influenza A (both H3 and H1) and influenza B virus.

The test most commonly used in the doctor’s office 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 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.

Influenza can also be diagnosed by the detection of antibodies in the patient’s serum. A rise in antibody titer of at least fourfold 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.

Other tests such as direct fluorescent antibody on respiratory specimens and virus isolation in cell culture can also be used.

Treatment

There are four drugs available for the treatment of influenza. Three drugs are neuraminidase inhibitors, namely oseltamivir, zanamivir, and peramivir. The fourth drug, baloxavir inhibits the endonuclease (ribonuclease) required for the synthesis of viral mRNA. It inhibits a process called “cap-snatching.” (See Table 38–3 and the paragraph below.) Amantadine is no longer used because many influenza A isolates are resistant.

Oseltamivir (Tamiflu) taken orally and zanamivir (Relenza) inhaled into the nose are the two most commonly used drugs for the treatment of influenza. A third drug, peramivir (Rapivab), is administered intravenously and became available in 2015. 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.

Resistance to Tamiflu occurs but currently is not clinically significant. Some isolates of H1N1 influenza virus are resistant to Tamiflu. However, H3N2 strains are still susceptible to Tamiflu. Both H1N1 and H3N2 strains remained susceptible to Relenza. All influenza B strains are susceptible to Tamiflu and Relenza.

Tamiflu pills are administered orally, whereas Relenza is delivered by inhaling the powder 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. These drugs are most effective when taken within 48 hours of the onset of symptoms. In 2015, some concern regarding the efficacy of Tamiflu and Relenza arose. Additional studies are needed to resolve this issue.

In 2018, the FDA approved a new drug, baloxavir marboxil, (Xofluza) for the treatment of influenza. The drug inhibits the “cap-snatching” ribonuclease required for the synthesis of influenza virus mRNA (see Figure 29–4). Only one oral dose is required and the drug should be given within the first 48 hours of symptoms for maximum effectiveness. It is effective against a wide range of influenza virus strains including oseltamivir-resistant strains. It is effective against both influenza A and influenza B viruses.

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 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.

Prevention

The main mode of prevention is the vaccine, which contains both influenza A and B viruses. The vaccine is usually reformulated each year to contain the current antigenic strains. A major research goal is to formulate a “universal vaccine” that will be effective against all antigenic variants. This would eliminate the need to reformulate the vaccine each year.

The vaccine contains the latest drift mutants that are selected in the Spring of the year for the vaccine to be administered in the Fall and Winter of that year. It takes approximately 6 months to prepare and safety test the new vaccine. This process is designed to induce immunity to the influenza virus strain most likely to cause disease that Winter. One problem with this 6 month process is that both the virus in the community and the virus in the vaccine being prepared continue to drift in the interim and in some years can result in significantly reduced vaccine efficacy.

There are two main types of influenza vaccines available in the United States, a killed vaccine and a live, attenuated vaccine (Table 38–4). Both a trivalent vaccine containing recent isolates of two A strains (H1N1 and H3N2) and one B strain and a quadrivalent vaccine containing two A strains and two B strains are available.

The vaccine most often used is the killed vaccine made in chicken eggs. 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. A high-dose killed vaccine that contains four times as much hemagglutinin as the standard vaccine is recommended for those over 65 years of age. A killed influenza vaccine that can be administered intradermally is also 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. There is no evidence of reversion to virulence.

This vaccine is administered by spraying into the nose (“nasal mist”). The live vaccine is recommended for children, whereas the inactivated vaccine is recommended for adults. The live vaccine should not be given to pregnant women or to immunocompromised individuals.

Note that in 2018, a new guideline stated that egg-allergic patients can be vaccinated safely with any flu vaccine with no special precaution, regardless of egg-reaction history. This changes the previous recommendation which was that anyone who has a significant allergy to chicken egg proteins (e.g., anaphylaxis) should not receive these vaccines. Note also that a killed influenza vaccine (Flucelvax) made in calf kidney cell culture is available for patients allergic to egg protein (see Table 38–4). This vaccine has two advantages: It contains no chicken proteins and it has a short turnaround time, so the latest drift mutant can be used.

In addition, a recombinant vaccine (Flublok) is available. This vaccine is made by inserting the gene encoding the viral hemagglutinin into an insect virus (baculovirus) that is propagated in insect cell culture. The insect cells produce the hemagglutinin of influenza virus. Flublok contains purified hemagglutinin as the immunogen without chicken egg proteins. This vaccine also has a short turnaround time and can be given to those with egg allergy.

The killed vaccine is not a good immunogen, because little IgA is made and the titer of IgG is relatively low. Protection wanes rapidly and typically 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 healthcare personnel who are likely to transmit the virus to those at high risk. Immunization of pregnant women with the killed vaccine is recommended as that decreases the risk of influenza in the newborn. Transplacental IgG protects the newborn during the first 6 months when the child is not capable of responding vigorously to the vaccine itself.

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 (Tamiflu), 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 (February 2016), 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. A vaccine against the H5N1 strain of influenza A virus is available.

H7N9 Influenza Virus

In 2013, an outbreak of influenza caused by an H7N9 strain of influenza virus A in humans occurred. Prior to this time, the H7N9 strain affected only birds, especially chickens. Annual outbreaks have occurred, up to and including 2017. A total of 1258 infections in humans have been documented, and 41% of these patients died. Cases have occurred primarily in 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. Candidate vaccines are being developed, but none are available as of this writing.

3. Swine Influenza Virus Infection in Humans

In April 2009, a novel swine origin strain of influenza A (H1N1) 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 February 2016, 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, which 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.

Diseases

Parainfluenza virus causes 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 (see Table 38–2). The surface spikes consist of hemagglutinin (H), neuraminidase (N), and fusion (F) proteins. 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

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

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, barking 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. A laboratory diagnosis can be made by detecting parainfluenza virus RNA in respiratory tract specimens by using a PCR-based assay. The diagnosis can also be made by isolating the virus in cell culture, by detecting viral antigens using fluorescent antibody, or by observing a fourfold or greater rise in antibody titer.

Treatment & Prevention

There is neither antiviral therapy nor a vaccine available.

Diseases

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 (see Table 38–2). Its surface spikes are fusion proteins, not hemagglutinins or neuraminidases. The fusion protein causes cells to fuse, forming multinucleated giant cells (syncytia), which give rise to the name of the virus (Figure 38–3).

Humans are the natural hosts of RSV. RSV has two serotypes, designated subgroup A and subgroup B. Antibody against the fusion protein neutralizes infectivity.

Summary of Replicative Cycle

Replication is similar to that of parainfluenza virus (see Swine Influenza Virus Infection in Humans).

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

A laboratory diagnosis can be made by detecting the RNA of RSV in respiratory tract specimens using a PCR-based assay. An enzyme immunoassay (“rapid antigen test”) that detects the presence of RSV antigens in respiratory secretions is also 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.

Treatment

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.

Prevention

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.

HMPV was first reported in 2001 as a cause of severe bronchiolitis and pneumonia in young children in the Netherlands. It is a member of the paramyxovirus family and, as such, is an enveloped virus with a single-stranded, nonsegmented, negative-polarity RNA genome. One of the spikes on its surface is a fusion protein that causes multinucleated giant cells in infected respiratory tract tissue. The fusion protein mediates attachment to the cell, and antibody against the fusion protein prevents infection. HMPV has two genotypes and several subtypes.

It is similar to RSV (also a paramyxovirus) in the range of respiratory tract disease it causes, namely, mild upper respiratory infections to bronchiolitis to severe pneumonia. Fever, coryza, wheezing, and cough are the most common symptoms. Serologic studies showed that most children have been infected by 5 years of age. Immunity is incomplete, and reinfection occurs despite development of an antibody response.

Laboratory diagnosis typically involves detection of viral RNA in respiratory tract samples by using a PCR assay. Treatment is supportive. There is no effective antiviral drug and no vaccine.

Diseases

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 (MERS) emerged in that area of the world. These pneumonias are caused by SARS coronavirus (SARS-CoV) and MERS coronavirus (MERS-CoV), respectively.

In December 2019, an outbreak of pneumonia in Wuhan, China caused by a new coronavirus was reported. This virus, now named SARS-CoV-2, is causing a world-wide pandemic. This virus and the disease it causes called COVID-19 are discussed separately in a section entitled “Coronavirus Outbreak and Global Pandemic in 2019-2020”.

Important Properties

Coronavirus has a non-segmented, single-stranded, positive-polarity RNA genome (see Table 38–2). It is an enveloped virus 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 (See Figure 38-4). A cross-sectional model of a coronavirus is shown in Figure 38-4.1. Note the spike proteins on the surface and the coiled RNA genome in the interior of the virion.

There are seven serotypes, four of which cause upper respiratory tract infections, such as the common cold. The other three cause lower respiratory tract infection, such as pneumonia. These three are SARS-CoV, SARS-CoV-2 and MERS- CoV. The antigenicity of the viral spike protein of these three viruses are different from each other. The antigenicity is relatively stable, although variants of SARS-CoV-2 have appeared during the pandemic.

The receptor for the SARS-CoV and SARS-CoV-2 on the surface of human cells is angiotensin-converting enzyme-2 (ACE-2). The other coronaviruses use different cell surface peptidases as their receptor.

Summary of Replicative Cycle

The replicative cycle begins when the spike protein on the surface of the virion binds to the receptor, often the ACE-2 protein, on the cell surface. A cell surface protease cleaves the spike protein to reveal a fusion protein that mediates entry into the cytoplasm, where the virion is uncoated. The positive-strand genome is translated into two large polypeptides, which are cleaved by two virus-encoded proteases into functional viral proteins. One of these proteins is the RNA polymerase that synthesizes both the progeny genome and the mRNAs that are translated into the structural proteins of the progeny virions. The mRNAs form a set of “nested” RNAs that are a characteristic feature of coronaviruses. The virus is assembled and obtains its envelope from the endoplasmic reticulum, not from the plasma membrane. Replication occurs in the cytoplasm.

Transmission & Epidemiology

Coronavirus is transmitted primarily by the respiratory route via sneezing and coughing. Transmission via contact of hands with contaminated surfaces also occurs. 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. This seasonality is less dramatic than that of influenza virus.

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 known to be “super-spreaders.” Early in the outbreak, many hospital personnel were affected, but respiratory infection control procedures greatly reduced the spread within hospitals.

There are many animal coronaviruses in both domestic and wild animals. 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 that region. The disease is called Middle East respiratory syndrome (MERS), and the virus is called MERS coronavirus (MERS-CoV). As of 2019, approximately 2400 cases of MERS have been reported with a mortality rate of 35%.

The closest relative of MERS-CoV is a bat coronavirus, and bats are thought to be a reservoir. Close contact with camels appears to be the mode of transmission to humans. The risk of person-to-person transmission is low but has occurred in hospitals with inadequate infection control.

Pathogenesis & Immunity

Infection by the “common cold” coronaviruses typically is 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, up to two years, and reinfection can occur.

Pneumonia caused by SARS-CoV is characterized by diffuse edema in the alveoli resulting in hypoxia. Infection by SARS-CoV-2 involves not only the lung but other organs as well. See the separate section on SARS-CoV-2 later.

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

If SARS or MERS is suspected, PCR-based tests that detect coronavirus RNA in respiratory tract specimens can be used. Antibody-based tests to detect a rise in antibody titer can be used for epidemiologic purposes.

Treatment & Prevention

There is no antiviral therapy available for SARS-CoV, MERS-CoV, or any of the common cold strains. Some antiviral drugs may effective against SARS-CoV-2 and are discussed in the next section.

There is no vaccine available against any coronavirus.

Coronavirus Outbreak and Global Pandemic in 2019-2021

Introduction to the Pandemic

In December 2019, an outbreak of pneumonia in Wuhan, China caused by a new, novel Coronavirus occurred. This virus is named SARS-CoV-2 and the disease is named COVID-19. (COVID stands for Coronavirus Infectious Disease and 19 stands for 2019.) The World Health Organization declared a global pandemic on March 11, 2020.

As of this writing on October 14, 2021, the virus has caused approximately 239 million cases, and more than 4.8 million deaths world-wide. The fatality rate is approximately 2.0%. In the United States, approximately 44 million cases and 712 thousand deaths have been reported. The fatality rate in the United States is approximately 1.6%. World-wide, approximately 6.4 billion vaccine doses have been administered.

As of June 2021, the number of cases and deaths from COVID-19 declined significantly, mostly as a result of widespread immunization. However, in July and August 2021, a fourth wave of infections occurred. This increase in infections is the result of three factors, waning immunity induced by the vaccine, the delta variant that has increased transmissibility, and relaxation of public health measures such as masking.

The fundamental reason why this virus caused a global pandemic is that it is a new (novel) strain of coronavirus to which the human population had no pre-existing immunity. The virus emerged from the animal population with spike protein antigens on its surface to which no one had antibodies.

Origin of the Novel Coronavirus

Based on genome RNA sequencing results, SARS CoV-2 closely resembles a coronavirus of bats and that animal is likely to be the natural reservoir. A second, intermediate reservoir, the pangolin, is likely to be involved. Sequences of the pangolin CoV spike protein are found in the SARS CoV-2 spike protein.

In May 2021, the original hypothesis that SARS-COV-2 spread from an animal to people at "wet animal" market in Wuhan, China was questioned. An alternative possibility that workers at the Virus Laboratory in Wuhan China may have been accidently infected and unintentionally spread the virus to others was raised.

Sequencing of the spike protein gene during the course of this pandemic revealed several mutations that are causing disease in many areas. For example, a mutation designated D614G in the gene encoding the spike protein favors an “open” configuration of the receptor binding domain on the spike protein thereby increasing the ability of the virus to infect the cell. The mutant D614G virus (also called G strain) was, at the time, the most common virus isolated from COVID-19 patients world-wide.

In December 2020, a new mutant strain designated B.1.1.7 (now known as Alpha variant) was reported to be spreading widely. This variant has 17 mutations, 8 of which are in the gene for the spike protein. This variant is more transmissible but not more virulent than the existing strain. Further, the current vaccines elicit antibodies that appear to be protective against this new variant. In April 2021, the B.1.1.7 variant became the dominant strain in the United States.

In January 2021, additional variants appeared in South Africa, Brazil, India, and in the United States. Initial studies showed that these variants have increased transmission, and may be more virulent, that is, cause death more frequently. In addition to the B.1.1.7 variant mentioned above, the B.1.351 (Beta) variant that emerged in South Africa, the P.1 (Gamma) variant that emerged in Japan and Brazil, and the B.1.617.2 (Delta) variant that emerged in India, are all circulating in the United States. The Delta variant is now the dominant strain in the United States. Recent studies have shown that two doses of the existing vaccines will provide reasonable protection against these new variants. These four variants, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) have been designated "Variants of Concern" by WHO and CDC.

Attachment and Entry of Virus into Cell

The main receptor for SARS CoV-2 is the ACE-2 receptor on the surface of respiratory tract epithelium. The spike protein on the surface of the virus binding to the ACE-2 receptor is the first step in the entry of the virus into the cell. After binding, the cell surface protease, TMPRSS-2, cleaves the spike protein to reveal a fusion sub-unit that mediates fusion of the virus with the cell membrane and entry of the virion into the cytoplasm.

Antibody to the virus elicited either by natural infection or by a vaccine (when available) neutralizes the virus by preventing the binding of the spike protein to the ACE-2 receptor. The relatively low number of cases of COVID-19 in children is attributed to the low number of the ACE-2 receptor displayed on their cells.

A second newly identified receptor on the cell surface is neuropilin-1 (NRP-1). The spike protein of the virus binds to NRP-1 and the virus can enter the cell. Antibody to NRP-1 prevents infection of the cell suggesting that it could be an additional target for drugs or vaccines.

Transmission

The primary mode of transmission is inhalation of respiratory droplets generated by coughing, sneezing, or talking during face-to-face contact. Respiratory aerosols also play important role in transmission of this virus. Note that aerosols are smaller than droplets so stay in the air longer and can be distributed over a distance more than 6 feet by air currents. Shedding of virus by an infected patient typically begins 2 to 3 days before symptom onset and lasts for about seven days. Shedding of virus prior to the appearance of symptoms explains the well-recognized phenomenon of asymptomatic transmission.

Transmission by hand contact with surfaces containing virus also occurs. Fingers transport the virus on the surface to the recipient’s eyes, nose, or mouth.

The majority of infections are acquired by transmission from asymptomatic carriers, probably by droplets/aerosols generated by talking, singing, or shouting. This indicates that a large amount of virus is present in the upper respiratory tract. People with asymptomatic infections are thought to be capable of transmitting the virus during a period that begins several days after the time of infection and lasts for about a week. A rough approximation is, therefore, about ten days after the time of infection.

Vertical transmission from an infected mother to the fetus is very rare. Transmission from an infected parent to a neonate is uncommon but can result in symptomatic COVID-19 disease in the neonate.

“Super-spreader” events at which large numbers of people have been infected have been observed. These typically involve large numbers of people gathering, often indoors, and not wearing masks or observing the 6 foot social distance. It is thought that ”super-spreading” is caused not by an individual producing exceptionally large amounts of infectious virus but rather by the combined effect of the environmental factors conducive to spread mentioned in the previous sentence.

Nursing homes, prisons, and homeless shelters have high rates of infection due to the crowded living conditions. Nursing homes in particular have many serious infections because the population is elderly.

Coronavirus infections exhibit less seasonality that do influenza virus infections. The increase in SARS CoV-2 infections in the summer of 2020 indicates that this coronavirus is not exhibiting a drop-off in infections during the warmer months the way influenza does. Nevertheless, a world-wide study performed in January to March 2020 indicated a correlation of outbreaks of COVID-19 within a narrow band of latitude with low temperature and low humidity.

Clinical Findings

The incubation period ranges from 2 to 14 days with a mean of 5 days. A quarantine period of 14 days has, therefore, been instituted.

The main clinical findings are fever, dry cough, and shortness of breath. Sore throat may occur but is not a prominent feature. Systemic symptoms such as fatigue, shaking chills, headache, and myalgia also may occur.

In addition to the respiratory tract, other organs such as the heart, kidney, brain, and gastrointestinal tract can be affected (see Table 38-5). A severe myocarditis with symptoms resembling a myocardial infarction has occurred in some patients. Loss of ability to smell (anosmia) and abnormal ability to taste (dysgeusia) are the initial symptoms in some patients. Anosmia and dysgeusia are important diagnostic features of COVID-19. Encephalopathy has also been observed. Nausea, vomiting, and diarrhea have occurred in some patients. Blood clots occur in some patients resulting in thrombosis or emboli leading to an increased risk of stroke.

Many of these findings are caused not by the virus directly but by the Cytokine Release Syndrome, also known as “Cytokine storm”. Viral infection triggers an overproduction of cytokines such as interferon-gamma, tumor necrosis factor, interleukin-6, bradykinin, and other pro-inflammatory cytokines (see Pathophysiology section below).

Other clinical findings include inflammation of the toes (“Covid toes”) and a Kawasaki disease-like syndrome that has occurred in children. The latter has been given the name “pediatric multisystem inflammatory syndrome”. It is also known as multisystem inflammatory syndrome in children (MIS-C). Another important clinical finding is is the observation that superimposed bacterial infections in the respiratory tract or blood occur in many patients.

Lymphopenia is common. Serum C-reactive protein and lactate dehydrogenase are elevated. Elevated D-dimers in the plasma occur in some patients resulting from clotting abnormalities. Respiratory tract specimens are typically negative for other respiratory viruses, including influenza virus.

Chest x-ray typically reveals bilateral opacities, often with a “ground-glass” appearance. No pleural effusions are seen. Mechanical ventilation is often required in patients with severe disease.

Death is due to hypoxemic respiratory failure. Cytokine storm contributes to death in some patients. A common listed cause of death is Acute Respiratory Distress Syndrome (ARDS).

Overall hospital mortality rates range from 15 to 20 but up to 40% for ICU admissions. Mortality rates differ greatly by age. The death rate per 1000 CVID-19 cases is 1.1 for those in the 18 to 29 year age group but 210.5 for those 75 to 84 years old and 304.9 for those 85 years or older.

In patients who have recovered from COVID-19 disease, the duration of antibody-mediated immunity appears to be at least 6 months. IgG antibody to spike protein was detectable for more than 6 months as were memory B cells. However, CD-4 positive T cells and CD-8 positive T cells declined with a half-life of 3 to 5 months.

Some patients who have recovered from the initial severe symptoms, continue to have symptoms, such as prolonged cough, shortness of breath, chest pain, joint pain, fatigue, dizziness, and confusion for several months. These after-effects cause significant limitations on the ability on the quality of life. This occurs in many who did not have prior pre-existing conditions, had mild initial disease, or were young adults. Some also continue to have positive PCR tests indicating that virus is still present. The World Health Organization has named this syndrome “Long COVID”. These patients are referred to as ”long haulers”. These long-term symptoms are also called “post-acute sequelae of SARS-CoV-2” abbreviated PASC. Approximately 37% of COVID-19 patients had one or more symptoms of Long COVID between 3 to 6 months after their diagnosis.

Approximately 50% of infections are asymptomatic and many others have only mild respiratory tract disease. Older adults (especially those over 70 years of age), people with compromised immunity, diabetics, and those with chronic heart, kidney, or respiratory tract disease are more likely to have serious COVID-19 disease. Obese people, specifically those with a body mass index or 30 or greater, are at high risk of serious disease. People with a history of smoking or vaping have a significant risk of severe COVID-19 disease.

In general, the symptoms of COVID-19 in children are less severe and death occurs much less often. This is attributed to two observations: that there are fewer ACE-2 receptors in children than adults and that children mount a stronger innate immune response than do older adults.

In August 2020, reports of reinfection began to appear. For example, a patient with documented COVID-19 infection in April 2020, recovered, and tested negative. In August, although asymptomatic, he tested positive again. Genome analysis revealed he was infected with two different clades of the virus.

Initial studies showed that people with ABO blood group A have a higher risk of contracting COVID-19 than people with the O group. This is attributed not to the presence of the A antigen but rather to the absence of the A antibody. It is speculated that A antibodies in the plasma of people who have O group may bind to sugars on the viral spike protein and inhibit entry of the virus into the cell. Recent studies have found that people with blood group A are not at much greater risk.

Men have more COVID-19 infections than women. This is attributed to the up-regulation by testosterone of TMPRSS-2, a protease on the cell surface involved with entry of the virus into the cell.

A disproportionate percentage of COVID-19 cases occurs in minority populations. For example, a report from the Centers for Disease Control and Prevention described a community in which 33% of COVID-19 patients were Black and 45% were White whereas the percentage in the community at large was 18% Black and 59% White.

Pathology

Microscopic examination of the lung tissue of deceased patients showed marked alveolar damage, edema, and infiltration of T lymphocytes. Severe endothelial damage was observed. Widespread thrombosis of capillaries was seen in many organs. Microangiopathy and angiogenesis were also observed.

Pathophysiology

The respiratory manifestations are likely to have two pathogenetic mechanisms: one is the killing of alveolar cells by the virus. Accumulated cell debris blocks diffusion of oxygen into the capillaries resulting in hypoxia.

The other is killing of the endothelial cells of the capillaries lining the alveoli. This triggers blood clots and an immune-mediated “cytokine storm” (also known as cytokine release syndrome) resulting in further damage to the alveolar membrane and acute respiratory distress syndrome (ARDS). High levels of pro-inflammatory cytokines such as IL-1, IL-6, bradykinin, and tumor necrosis factor (TNF) are found.

Damage to endothelial cells and the resulting blood clots is the cause of many of the extra-respiratory manifestations of COVID-19 disease.

SARS CoV-2 inhibits interferon synthesis, an important part of the innate immune response. The N (nucleocapsid) protein blocks the action of the RIG receptor that detects dsRNA in the cytoplasm thereby inhibiting interferon synthesis.

Laboratory Diagnosis

There are three types of laboratory tests. Two of these detect the presence of the virus, either by PCR test detecting the viral RNA or by enzyme immunoassay detecting a viral antigen. The third type of test detects antibodies to the virus in a person’s serum.

Laboratory diagnosis for the presence of viral RNA is made by PCR testing on respiratory tract specimens, such as nasopharyngeal swabs. Although very sensitive and specific, PCR test can be falsely-negative if the specimen is taken too soon after infection. The test is most sensitive at 3 days after symptom onset. A rapid isothermal amplification assay for use in the field has been developed. This test does not require cycles of heating and cooling. A CRISPR-based test for the presence of virus has also been developed.

Rapid laboratory tests for viral antigen, typically the spike protein, are also available. These enzyme immunoassay tests are not as sensitive as PCR tests so false-negative results can occur. A negative result does not rule out infection. The advantage of this type of test is that they are rapid, inexpensive, and can be done by the user at home, much like a pregnancy test. In August 2020, the FDA approved a “point-of-care” antigen test that detects the nucleocapsid antigen of SARS-CoV-2 using a nasal swab specimen. As of this writing, several antigen tests such as BinaxNOW, QuickVue, and Flowflex, are available. Inexpensive home tests that provide rapid results seem likely to be important tools to identify those who are infected and therefore need to quarantine.

Tests to detect IgM and IgG antibodies to the virus have become available. IgM antibodies can be detected by 5 days after infection but IgG antibodies are first detected 14 days after symptom onset. Note that these tests indicate an antibody response but they do not indicate that the virus is present at the time of the test. A positive test indicates that the person has been infected but not that the person can transmit the virus to others.

Antibody tests have greater than 95% specificity. Tests that detect total (IgM and IgG) antibody are the most sensitive. There is a question about which antigen, the nucleocapsid (NC) protein or the spike protein (or both) should be used in the tests. The nucleocapsid (NC) protein is most abundant so testing for that protein would be most sensitive. But tests that detect antibody to the spike protein are most likely to detect neutralizing antibody.

Another question is how long antibody elicited by infection, as distinct from immunization, will protect from reinfection. In July 2020, a study reported that patients with mild disease showed a rapid decline in antibody titer during the 3 months following recovery. Note that the duration of detectable antibody in patients from the SARS outbreak in 2003 lasted about 2 to 3 years.

PCR tests for viral RNA are likely to be positive during the first week of symptomatic infection but antibody tests are likely to be positive only after 3 weeks of symptomatic infection. It is recommended that people wait at least 3 weeks after symptoms appear to have antibody testing done.

PCR tests are currently reported as either positive or negative, not as the viral load as is done with HIV infection. There is a proposal to report the Cycle Threshold (CT) as an indirect measure of the amount of virus present in the patient’s specimen. The PCR test undergoes repeated cycles of heating and cooling hence the use of the term “Cycle”. If no viral RNA is detected after 40 cycles, the test is reported as negative, Note that if the specimen turns positive at a low CT then there is a large amount of virus present. Knowing this would be helpful in evaluating how likely the patient was to transmit this virus to others.

Treatment

Supportive care including supplemental oxygen should be instituted. Some hospitalized patients need respiratory support provided by mechanical ventilators. Prone positioning helps patients to breathe.

Therapeutic treatment modalities fall into four categories. There are drugs directed against viral replication, antibodies directed against viral replication, drugs directed against cytokine storm and antibodies directed against cytokine storm (see Table 38-6).

On October 22, 2020, the FDA approved the use of remdesivir in hospitalized patients. Clinical trials showed that remdesivir shortened the hospital stay of seriously ill patients by 4 days and decreased mortality from 11% to 7%. Remdesivir is an adenosine analogue that inhibits viral RNA-dependent RNA polymerase. It is a “chain-terminating” drug. Favipiravir, another RNA polymerase inhibitor, is also being tested. Hydroxychloroquine, the anti-malarial drug, is not effective. There is no published data on the effectiveness of oleandrin.

In addition to the viral polymerase, a second drug target is the virus-encoded protease. Unfortunately, a trial of the protease inhibitor combination lopinavir/ritonavir reported no clinical improvement. A trial of the protease inhibitor, atazanavir, is in progress.

In August 2020, the use of convalescent plasma received emergency use authorization from the FDA. Clinical trials using convalescent plasma to treat COVID-19 are ongoing. Preliminary data shows this may be helpful, but results from larger studies are needed. Note that plasma is being used, not hyperimmune globulins. Note also that the plasma must be matched to the recipient as anti-ABO antibodies are present in the plasma.

Humanized monoclonal antibodies can be used for either treatment and prevention. Monoclonal antibodies avoid the risk of using human plasma which may transmit viruses in the donor plasma. On November 9,2020, the FDA approved emergency authorization for bamlanivimab, an IgG monoclonal antibody directed against the spike protein of SARS CoV-2. It should be used to treat those who have tested positive, have mild-to moderate disease, and are at risk of developing severe disease. It is not for hospitalized patients with severe disease.

On November 21, 2020, the FDA granted emergency use authorization (EUA) for a combination of two monoclonal antibodies (casirivimab and imdevimab) for the treatment of mild to moderate COVID-19. These two antibodies bind to different areas on the Receptor Binding Domain of the spike protein. In February 2021, the FDA approved an EUA for the use of a second monoclonal antibody combination containing bamlanimumab and etesevimab. These monoclonal antibodies target different sections of the receptor binding domain of the spike protein.

Nanobodies are single domain antibodies composed of the variable region of the heavy chain of an immunoglobulin. Their small size makes them very stable, an attribute that allows delivery via aerosol into the respiratory tract. Nanobodies directed against the CoV spike protein (termed Aeronabs) are being considered for either treatment of early disease or for prophylaxis.

A trial of intra-nasal interferon-beta showed treated patients were significantly more likely to recover than patients who did not receive the drug.

Regarding the treatment of cytokine storm, both dexamethasone, a corticosteroid, and tocilizumab, a monoclonal antibody against the interleukin-6 (IL-6) receptor, are approved for use. One recommended regimen consists of dexamethasone with or without remdesivir plus either tocilizumab or baricitinib, a Janus kinase inhibitor (see next paragraph).

Baricitinib and ruxolitinib (Janus kinase (JAK) inhibitors), are also being evaluated as an inhibitor of cytokine release. A combination of baricitinib and remdesivir reduced time to recovery in hospitalized patients in a recent clinical trial. On November 19, 2020, the FDA granted emergency use authorization (EUA) for the combination of baricitinib and remdesivir.

Antioxidant compounds, such as glutathione (GSH) and N-acetyl cysteine inhibit NF kappa-B, a proinflammatory transcription factor. A trial using GSH to treat ARDS has shown some efficacy. Mesenchymal stem cell therapy is also undergoing clinical trial to reduce the effects of cytokine storm.

Prevention

There are three vaccines that have received an Emergency Use Authorization (EUA) as of February 27, 2021. On December 11, 2020, the FDA approved the Pfizer m-RNA vaccine and one week later an EUA for the Moderna m-RNA vaccine was granted. Both vaccines contain the mRNA for the coronavirus spike protein enclosed in a lipid nanoparticle. On August 23, 2021, the FDA gave full approval to the Pfizer vaccine.

On February 27, 2021, the FDA approved an EUA for the Johnson & Johnson vectored vaccine. This vaccine contains a replication-deficient human adenovirus into which the DNA encoding the spike protein of SARS CoV-2 has been inserted. Table 38-7 describes the leading vaccines that have either received an EUA or are in advanced clinical trials.

Note that these vaccines are monovalent and stimulate an immune response to the spike protein of the original strain of SARS CoV-2. To address the emergence of new viral variants, multivalent vaccines and booster doses are being prepared.

As of August 2021, a third dose (booster dose) of the two mRNA vaccines is being administered to immunocompromised people. Because of waning immunity and the surge of delta variant cases, booster doses are planned for the general population in September 2021. On September 22, 2021, the FDA approved a booster dose for those who received two doses of the Pfizer vaccine at least 6 months previously and were at least 65 years or older or had a high risk for severe COVID-19. Booster doses for the Moderna mRNA vaccine and for the Johnson & Johnson vectored vaccine are expected to be approved shortly.

The effectiveness of the vaccines to induce neutralizing antibody, to prevent transmission by inducing IgA, and the duration of its protection are important aspects. The short term and long term safety of the vaccines must be evaluated.

Despite a vaccine effectiveness of 80 to 90 % in preventing severe COVID disease, people immunized with two doses nevertheless have contracted COVID-19 disease. In most cases, this "breakthrough" disease was mild, although in some, it was severe and a few patients died.

An unusual adverse effect of these m-RNA vaccines is a rash at or near the site of infection called "COVID-Arm. It appears to be a delayed hypersensitivity response to some component of the vaccine. Onset of the rash occurred approximately 8 days after inoculation and the rash resolved without sequelae. Most patients did not experience a rash upon receiving the second dose but a few did.

Monoclonal antibodies can be used for prevention as well as treatment. These antibody preparations can be used either pre-exposure in people working in high risk situations or post-exposure in people known to be exposed to the virus. These antibodies can provide immediate protection that can last for weeks to months. The FDA has issued an EUA for two monoclonal antibody combinations, casirivimab/imdevimab and bamlanivimab/etesevimab, for prophylaxis in a person who had close-contact with a COVID-19 patient.

Prevention centers on public health and hygiene measures to interrupt transmission. Wearing a mask and social (physical) distancing at least 6 feet are the most important measures. Other basic measures include frequent hand washing, practicing cough and sneeze etiquette, avoiding touching eyes, nose, and mouth, avoiding people with respiratory symptoms, and staying at home if you are sick.

Those infected should be isolated. Isolation should be maintained for at least 10 days after onset of symptoms. Those who have been exposed but who are not known to be infected should be quarantined for 14 days.

Contact tracing to identify those who have been exposed is another important tool to interrupt the chain of transmission. Personal protective equipment (PPE) for medical personnel is essential to interrupt transmission in hospitals.

In the global pandemic of 2020, many schools and colleges were closed or classes presented remotely. Large gatherings such as sporting events and concerts were cancelled or postponed. Many states issued “Stay at Home” orders, allowing only essential services to remain open.

The safe transition to the “New Normal” will depend on the presence of antibodies in the individual acquired either by the infection or by the vaccine. If enough people develop immunity, then herd immunity may protect those who are still susceptible. The percentage of immune people required to develop effective herd immunity against SARS-CoV-2 is unknown at this time.

Whether this virus becomes endemic and recurs at regular intervals or, like the SARS-2003 coronavirus no longer causes disease in humans, remains to be seen.

Disease

This virus is the main cause of the common cold.

Important Properties

Rhinovirus has a nonsegmented, single-stranded, positive-polarity RNA genome. It is a nonenveloped virus with an icosahedral nucleocapsid. There is no polymerase within the virion (see Table 38–2).

There are more than 100 serologic types, which explains why the common cold is so common. They replicate better at 33°C than at 37°C, which explains why they affect primarily the nose and conjunctiva rather than the lower respiratory tract. Because they are acid-labile, they are killed by gastric acid when swallowed. This explains why they do not infect the gastrointestinal tract, unlike the enteroviruses. The host range is limited to humans and chimpanzees.

Summary of Replicative Cycle

Rhinovirus replication begins with the attachment of the infecting virion to a cell surface receptor called intercellular adhesion molecule-1 (ICAM-1). The virion enters the cytoplasm, and the capsid proteins are then removed (uncoated). After uncoating, the genome RNA functions as mRNA and is translated into one large polypeptide. This polypeptide is cleaved by a virus-encoded protease to form both the capsid proteins of the progeny virions and several noncapsid proteins, including the RNA polymerase that synthesizes the progeny RNA genomes. Replication of the genome occurs by synthesis of a complementary negative strand, which then serves as the template for the positive strands. Some of these positive strands function as mRNA to make more viral proteins, and the remainder become progeny virion genome RNA. Assembly of the progeny virions occurs by coating of the genome RNA with capsid proteins. Progeny virions accumulate in the cell cytoplasm and are released upon death of the cell.

Transmission & Epidemiology

There are two modes of transmission for these viruses. In the past, it was accepted that they were transmitted directly from person to person via aerosols of respiratory droplets. However, now it appears that an indirect mode, in which respiratory droplets are deposited on the hands or on a surface such as a table and then transported by fingers to the nose or eyes, is also important.

The common cold is reputed to be the most common human infection, although data are difficult to obtain because it is not a well-defined or notifiable disease. Millions of days of work and school are lost each year as a result of “colds.” Rhinoviruses occur worldwide, causing disease particularly in the fall and winter. The reason for this seasonal variation is unclear. Low temperatures per se do not predispose to the common cold, but the crowding that occurs at schools, for example, may enhance transmission during fall and winter. The frequency of colds is high in childhood and tapers off during adulthood, presumably because of the acquisition of immunity.

A few serotypes of rhinoviruses are prevalent during one season, only to be replaced by other serotypes during the following season. It appears that the population builds up immunity to the prevalent serotypes but remains susceptible to the others.

Pathogenesis & Immunity

The portal of entry is the upper respiratory tract, and the infection is limited to that region. Rhinoviruses rarely cause lower respiratory tract disease, probably because they grow poorly at 37°C.

Immunity is serotype-specific and is a function of nasal secretory IgA rather than humoral antibody.

Clinical Findings

After an incubation period of 2 to 4 days, sneezing, nasal discharge, sore throat, cough, and headache are common. A chilly sensation may occur, but there are few other systemic symptoms. The illness lasts about 1 week. Note that other viruses such as coronaviruses, adenoviruses, influenza C virus, and Coxsackie viruses also cause the common cold syndrome.

Laboratory Diagnosis

A laboratory diagnosis can be made by detecting the RNA of rhinoviruses in respiratory tract specimens using a PCR-based assay. Serologic tests are not done as there are too many serotypes.

Treatment & Prevention

No specific antiviral therapy is available. Vaccines appear impractical because of the large number of serotypes. Paper tissues impregnated with a combination of citric acid (which inactivates rhinoviruses) and sodium lauryl sulfate (a detergent that inactivates enveloped viruses such as influenza virus and RSV) limit transmission when used to remove viruses from fingers contaminated with respiratory secretions. High doses of vitamin C have little ability to prevent rhinovirus-induced colds. Lozenges containing zinc gluconate are available for the treatment of the common cold, but their efficacy remains uncertain.

Diseases

Adenovirus causes a variety of upper and lower respiratory tract diseases such as pharyngitis, conjunctivitis (“pink eye”), the common cold, and pneumonia. Keratoconjunctivitis, hemorrhagic cystitis, and gastroenteritis also occur. Some adenoviruses cause sarcomas in rodents.

Important Properties

Adenoviruses are nonenveloped viruses with double-stranded linear DNA and an icosahedral nucleocapsid (see Table 38–2). They are the only viruses with a fiber protruding from each of the 12 vertices of the capsid. The fiber is the organ of attachment and is a hemagglutinin. When purified free of virions, the fiber is toxic to human cells.

There are 41 known antigenic types; the fiber protein is the main type-specific antigen. All adenoviruses have a common group-specific antigen located on the hexon protein.

Certain serotypes of human adenoviruses (especially 12, 18, and 31) cause sarcomas at the site of injection in laboratory rodents such as newborn hamsters. There is no evidence that adenoviruses cause tumors in humans.

Summary of Replicative Cycle

After attachment to the cell surface via its fiber, the virus penetrates and uncoats, and the viral DNA moves to the nucleus. Host cell DNA-dependent RNA polymerase transcribes the early genes, and splicing enzymes remove the RNA representing the introns, resulting in functional mRNA. (Note that introns and exons, which are common in eukaryotic DNA, were first described for adenovirus DNA.) Early mRNA is translated into nonstructural proteins in the cytoplasm. Progeny viral DNA genomes are synthesized by a virion-encoded DNA polymerase in the nucleus. After viral DNA replication, late mRNA is transcribed and then translated into structural virion proteins. Viral assembly occurs in the nucleus, and the virus is released by lysis of the cell, not by budding.

Transmission & Epidemiology

Adenoviruses are transmitted by several mechanisms: aerosol droplet, fecal–oral route, and direct inoculation of conjunctivas by tonometers or fingers. The fecal–oral route is the most common mode of transmission among young children and their families. Many species of animals are infected by strains of adenovirus, but these strains are not pathogenic for humans.

Adenovirus infections are endemic worldwide, but outbreaks occur among military recruits, apparently as a result of the close living conditions that facilitate transmission. Certain serotypes are associated with specific syndromes (e.g., types 3, 4, 7, and 21 cause respiratory disease, especially in military recruits; types 8 and 19 cause epidemic keratoconjunctivitis; types 11 and 21 cause hemorrhagic cystitis; and types 40 and 41 cause infantile gastroenteritis).

Pathogenesis & Immunity

Adenoviruses infect the mucosal epithelium of several organs (e.g., the respiratory tract [both upper and lower], the gastrointestinal tract, and the conjunctivas). Immunity based on neutralizing antibody is type-specific and lifelong.

In addition to acute infection leading to death of the cells, adenoviruses cause a latent infection, particularly in the adenoidal and tonsillar tissues of the throat. In fact, these viruses were named for the adenoids, from which they were first isolated in 1953.

Clinical Findings

In the upper respiratory tract, adenoviruses cause infections such as pharyngitis, pharyngoconjunctival fever, and acute respiratory disease, characterized by fever, sore throat, coryza (runny nose), and conjunctivitis. In the lower respiratory tract, they cause bronchitis and atypical pneumonia. Hematuria and dysuria are prominent in hemorrhagic cystitis. Gastroenteritis with nonbloody diarrhea occurs mainly in children younger than 2 years of age. Most adenovirus infections resolve spontaneously. Approximately half of all adenovirus infections are asymptomatic.

Laboratory Diagnosis

The most common method of laboratory diagnosis is a PCR-based assay that detects the DNA of adenoviruses in respiratory tract specimens. In addition, adenoviruses can be isolated in cell culture and detected by fluorescent antibody techniques. The detection of a fourfold or greater rise in antibody titer to adenoviruses can also be used.

Treatment

There is no antiviral therapy.

Prevention

Three live, nonattenuated vaccines against serotypes 4, 7, and 21 are available but are used only by the military. Each of the three vaccines is monovalent (i.e., each contains only one serotype). The viruses are administered separately because they interfere with each other when given together. The vaccines are delivered in an enteric-coated capsule, which protects the live virus from inactivation by stomach acid. The virus infects the gastrointestinal tract, where it causes an asymptomatic infection and induces immunity to respiratory disease. This vaccine is not available for civilian use.

Epidemic keratoconjunctivitis is an iatrogenic disease, preventable by strict asepsis and hand washing by healthcare personnel who examine eyes.