key: cord-267194-i6vetquk authors: Carman, William F.; Mahony, James B. title: The pathogens date: 2007-10-31 journal: Journal of Clinical Virology DOI: 10.1016/s1386-6532(07)70003-3 sha: doc_id: 267194 cord_uid: i6vetquk nan Respiratory viruses are important to human health at all levels. They account for a substantial proportion of visits to family practitioners, for short term sickness, absence from work, for outbreaks in institutions like old age homes, schools and military barracks, and for exacerbations of chronic illnesses such as asthma and COPD and, perhaps most critically, for serious illnesses that require hospitalisation in both the immunocompetent and the immunocompromised. Apart from a few unusual zoonotic pathogens such as SARS and avian influenza, they are transmitted between people, often amongst children with adults being infected if they come into contact with children. They are transmitted either from contact (skin to skin or fomites) or via airborne particles. The relative importance of these transmission modalities is unknown. These viruses are generally short-lived, ranging from minutes to hours on surfaces, but their high concentration means that they are likely to be transmitted. The number of people infected from each infected person is unknown. Vaccines and antivirals are largely unavailable or unproven, except against influenza. The outcome of infection is generally fine, although life-threatening illness can occur, usually for unknown reasons, even in the immunocompetent. Why some people get severe disease and others brush off the same virus with impunity is an intriguing area for future study. One has to assume it is due to innate and adaptive immune responses. The other field of discovery and rapid progress is diagnostics, the subject of this journal issue. A consensus has appeared that nucleic acid testing is here to stay and that it is preferable to other, old-fashioned approaches. The sensitivity is significantly better, although this is associated with questions regarding the clinical impact of that piece of RNA or DNA. With the ability to multiplex large numbers of targets in a single tube comes the possibility, not only to study the importance of mixed pathogens, but to link together two aspects of study -which virus is it and what is the host doing to clear it? All the viruses described below are important. They all have an ability to lay low families on a regular basis; they can cause severe and even fatal disease in children; they are spread in hospitals; they are a significant cause of lower respiratory tract illness in otherwise healthy adults; and, an often minor disease in children or adults can be spread to the immunologically weak, leading to severe and even life threatening disease. In some people who have a predilection for a severe outcome without an obvious reason, one assumes there is an unknown immunological reason. Every year, we see patients in ITU with one or more of these viruses and each time the clinician is surprised. The value of accurate and timely diagnosis is obvious in terms of patient management. Much is known about some respiratory viruses, in particular influenza, parainfluenza (PIV) and respiratory syncytial virus (RSV). Rhinoviruses are being increasingly regarded as significant pathogens. Here follows a brief introduction of each and how commonly and when they are seen in our two laboratories, one in Canada and one in Scotland. Influenza has three types (A, B and C). Flu A has numerous subtypes, defined by the specific varieties of haemagglutinin and neuraminidase molecules it has embedded in its envelope. Many of these varieties are seen only rarely in humans -humans predictably are infected by viruses with H1, 2 or 3 and N1 or 2. Flu A has yearly outbreaks, which can occur at any time between September and March. These outbreaks occur in a semi-immune population and are due to evasion of the immune system by the same subtype of the virus by mutation, mainly of the haemagglutinin. Occasionally, a new virus subtype is introduced from other animals or birds into humans, which leads to a worldwide epidemic, or pandemic. Well documented pandemics occurred in 1890, 1900, 1918, 1957 and 1968. Flu A tends to mutate linearly, but building on the previous lineage, every few years leading to a virus which has escaped the immune system. Flu B is found in most years but not all years, and it unusually causes the predominant outbreak. Most years it occurs either before or after the flu A outbreak. Although it is said to cause milder illness than flu A it is not clear how solid, or recent, the evidence base is for this assertion. Flu B has a number of lineages co-circulating and more than one can evolve simultaneously. Not much is known of flu C, except that multiple lineages circulate independently, but with the introduction of PCR, this virus is being found more frequently. Each year, influenza infects about 25% of the population, but probably half of this is asymptomatic. Influenza can be very unpleasant, especially if one is old or very young, for whom it can be fatal. Depending upon the virulence of the strain, the immunocompetent adult can either shake it off or will have to take to his or her bed for a week. Much heard is the comment that "I haven't had flu for years", but serology belies this. Influenza is a relatively easy diagnosis when it is circulating, but very difficult when it is not. Antiviral trials have revealed the primary care physicians are correct about 60% of the time in their clinical diagnosis in the middle of an outbreak. The corollary is that they are usually wrong when flu is not circulating! Cough, fever and presentation within 36 hours of onset is highly predictive of influenza. Without this triad of clues, if one is to prescribe antivirals, which are influenza specific, then one has to either know flu is circulating and still be prepared to over-prescribe by a third, or do a diagnostic test. If a test is ordered, the result needs to be available that day if a significant impact is to be achieved. Treatment initiated within 12 hours is significantly more effective compared to 48 hours. Diagnosis is particularly important in a hospital setting. Influenza pneumonia is difficult to clinically separate from other "atypical" pneumonias, yet the treatment is radically different. Parainfluenzaviruses have 5 types -1, 2, 3, 4a and 4b. They have a variable seasonal distribution, PIV 3 being predominantly Spring/Summer and PIV 1 and 2 being Autumnal. PIV 1 and 2 can alternate each year. These are largely childhood viruses, causing colds or croupy coughs (they are by far the commonest cause of croup) and bronchitis. They are the second most important cause of admission for respiratory disease in children (after RSV). Practically everyone gets PIV infections during childhood, such that adult infections are re-infections. Consequently, in adults, who tend to get infected from their children, the disease is usually an URTI, and it is only a problem in an immunosuppressed person, in particular after a transplant, becomes infected. Although the outcome is usually nonfatal, this depends upon the degree of immunosuppression. Mortality is significant if the infection leads to pneumonia. Perhaps such infections may be worse for the person in the next bed who may be more immunosuppressed and who gets a larger infecting dose because of their proximity to a person with a virus out of control. Control of infection, and knowing which virus is infecting a patient in a ward setting, is therefore very important. Not much is known about PIV 4. One study over 6 years revealed 13 of 367 PIV were PIV 4; 12/13 had respiratory illness and 1 had meningitis. Ten of the 12 were admitted for lower respiratory tract infection. Nine of the ten were under 24 months. The tenth was 7 years old and was immunocompromised. A recent case seen by one of the authors in an adult requiring coronary artery bypass surgery, who had severe pneumonia post-surgery (he caught it from his children before admission to hospital), shows that this pathogen can be very dangerous (paper submitted). RSV is very similar to PIV in that it is a childhood illness that spills over into the adult population as a cold (though often severe, with a cough), or as an exacerbation of COAD, but may have a particularly bad outcome in the immunosuppressed. There are two groups -A and B -and a number of subtypes, but most data show no association with severity. They are antigenically quite diverse. Often, both types co-circulate. Re-infections are very common, even in successive years. Like PIV, the subsequent infections are usually not as severe. RSV classically causes LRTIin particular bronchiolitis and pneumonia -in infants on a yearly basis. Year after year, around Christmas in the northern hemisphere, RSV infects a substantial proportion, probably about half, of that year's crop of babies and then largely disappears after 6 weeks, although a tail of infection can linger for many weeks. The next year, the other half becomes infected. RSV is almost unique in this behaviour. On the equator, infections can occur all year. Some hospitals screen all babies admitted for whatever reason and attempt to cohort the infected after admission -a significant number of asymptomatic infections are discovered. RSV is extremely common in family members of an infected baby. The role of RSV in mixed infections is important. Recent data reveal that the severity of an illness in which RSV is in a mixed infection is the same as if RSV is found alone. Rhinoviruses are everywhere. They are easily transmitted (like all these other viruses), not only because children have runny noses and smear the mucus over every available surface, including their parents, but because there are over 100 serotypes and the only way a virus can survive, except in a −70 freezer, is to be transmitted constantly between its hosts. For over 100 serotypes to survive means a lot of transmission. Using culture, children get 1.2 infections a year and adults 0.7; with the advent of PCR, this is likely to be much higher. There are two groups: the major group, containing >90%, which share a receptor and a minor group which use an alternative receptor. Usually, infection with one serotype leads to lifelong immunity. Antigenic evolution occurs but is not thought to play a major role in pathogenesis. Rhinoviruses are often found as mixed infections leading to studies to try to delineate their relative importance. They do infect the immunosuppressed, but in our experience, they generally do not cause life-threatening disease. In a number of occasions, patients can have a severe lower respiratory tract infection, with no bacteriological cause and the only pathogen found is rhinovirus. The patient usually recovers. They play an important role in exacerbations of asthma and COAD. They are also the next most important cause of bronchiolitis after RSV. Enteroviruses are commonly cited as causes of respiratory infection, mostly URTI. A problem arises with taxonomy: rhinoviruses and enteroviruses are probably part of a continuous spectrum of related viruses and related diseases. Enteroviruses per se can cause all of the respiratory diseases that we have discussed for all the other viruses, underlying the utility of improved and broad-ranging diagnostics. They are often mild and cause up to 15% of such illnesses in which a pathogen is found. Of course, with the improvement of diagnostic approaches, the total number of findings of an enterovirus is likely to increase but the overall percentage in which it is a cause will go down. Bronchiolitis is uncommon, but pneumonia occurs and is often severe. It is more likely in younger children and infants (in whom enteroviruses are more common anyway). Echoviruses 22 and 23 have been re-classified as Parechoviruses: the most likely disease manifestation is respiratory. The importance of the enteroviruses is as a differential diagnosis in severe LRTI in the young as antibiotics may not be needed. Clinical virology was boring for laboratories during the early 1990s with the last important virus being discovered nearly a decade earlier. Things changed dramatically in the late 1990s with the unexpected emergence of the first of several new respiratory viruses that emerged between the years 1997 and 2005. In 1997 influenza A H5N1 infected humans for the first time, in Hong Kong. Human metapneumovirus (hMPV) was discovered by Bernadette van den Hoogen and colleagues while looking at retrospective specimens for new respiratory viruses in patients where no respiratory viruses had been detected ( Van den Hoogen et al., 2001) . In November of 2002 in Quangdong Province in China, SARS-CoV first infected a restaurant chef. The source of infection was likely a palm civet that was prepared for restaurant patrons. SARS-CoV was brought to Hong Kong by a vacationing woman and Hong Kong quickly became the epicenter spreading the infection to 18 countries in a matter of months (WHO, 2004) . Additional avian influenza viruses emerged in the years following H5N1 viruses, including H7N7 in the Netherlands and H7N3 in Canada. In 2004 HCoV NL63 was discovered by Lia van der Hoek and her colleagues in Amsterdam, the Netherlands (van der Hoek et al., 2004) . The second new HCoV to be discovered since SARS-CoV was HKU1, discovered by Patrick Woo and his colleagues in Hong Kong in 2005 (Woo et al., 2005) . Neither of these HCoV were acquired by transmission from animals, and they are now thought to have been circulating in the human population for many years. In September 2005 Tobias Allander and colleagues at the Karolinska Institute in Sweden reported the discovery of a new human Parvovirus called Bocavirus (Allander et al., 2005) . Mimivirus was first discovered by La Scola and coworkers in 2003 in amoeba and there is growing evidence that it may be a true respiratory pathogen (La Scola et al., 2005) . Parvovirus 4 was first detected by Jones et al. in 2005 in plasma specimens and subsequently in respiratory tract specimens (Jones et al., 2005) . In the past quarter century, approximately 15 new viruses have been discovered that cause disease in humans, but none with such alarm as the Asian lineage of high pathogenicity known as H5N1 virus. The first introduction of H5N1 into the human population occurred in Hong Kong in 1997 and resulted in the death of 6 of 18 documented cases (Subbarao et al., 1998) . Exposure to infected chickens proved to be the important risk factor in all cases and no human to human transmission was documented. However, there is some serological evidence that asymptomatic or mild infection of household contacts did occur (Katz et al., 1999) . Culling of 1.5 million chickens in the Hong Kong markets was successful in stopping the outbreak. This represented the first proven outbreak of influenza that came directly from an avian source without reassortment of virus by antigenic shift. Subsequent outbreaks of human infections followed shortly thereafter with HPAIV H7N7 and H7N3 moving from domestic poultry to man in the Netherlands and Canada. In February 2003, H5N1 returned with two members of a family from Hong Kong being diagnosed following a visit to Fujian Province in China. One family member died. By late 2003, H5N1 had returned with a vengeance, infecting and killing millions of wild and domesticated birds in several countries of Southeast Asia including Cambodia, China, Japan, Indonesia, Laos, Malaysia, Thailand and Vietnam. Transmission to humans continued to increase wherever there was direct contact with infected domestic poultry and by June 2007 there were at least 313 infections and 191 deaths due to H5N1. Almost all of the human cases have had a clear history of exposure to infected poultry. Some epidemiological evidence has suggested than human to human transmission of H5N1 has occurred heightening the possibility of a possible pandemic (Ungchusak et al., 2005) . Human metapneumovirus was discovered in 2001 in the Netherlands ( Van den Hoogen et al., 2001) . This Pneumovirus belongs to the Paramyxoviridae family and resembles RSV in many regards including in its clinical presentation. hMPV outbreaks occur predominantly in the winter and spring months in temperate climates often overlapping or following the winter RSV outbreak. Some studies however, have shown that sporadic hMPV infections can occur year round. Most children are infected by the age of five years but infections can occur in all age groups. In studies where detection of hMPV was compared across several seasons, investigators have found significant differences from year to year. The incubation is thought to be 3 to 5 days. Formal transmission studies have not been reported but transmission is believed to occur by contact with respiratory secretions involving large particle aerosols, droplets or contaminated surfaces. Nosocomial infections have been reported. The period of viral shedding has not been determined but may be weeks following primary infection in infants. hMPV causes both upper and lower tract infections and the signs and symptoms are very similar to those caused by RSV ranging from mild rhinorrhea associated with common colds to severe cough, wheezing, bronchiolitis and pneumonia (Konig et al., 2004; Van den Hoogen et al., 2001) . Little can be said about the SARS epidemic that has not already been written. In just a few months the virus spread from Quangdong Province to Hong Kong and from the ninth floor of a hotel in Hong Kong to 18 countries around the world resulting in almost 8,000 infections and 776 deaths with a mortaility rate of 10% (WHO). The natural history of SARS-CoV has been documented in several studies. The initial symptoms are unremarkable and common to all upper respiratory tract viral infections. A few days of cough and low grade fever progresses rapidly to a full blown pneumonia requiring hospitalization and often mechanical ventilation. Fever, malaise, lymphopenia, elevated liver enzymes, together with infiltrates and consolidation on chest X-ray are usually present. Quantitative polymerase chain reaction (PCR) studies have shown that the viral load is high in the lower respiratory tract but low in the upper respiratory tract. Viral load in the upper respiratory tract and feces is low during the first 4 days and peaks at around day 10 of illness (Poutanen et al., 2003) . This is in marked contrast to other respiratory viral infections such as influenza that peak soon after the onset of symptoms. This unusual feature of SARS-CoV infection explains its low transmissibility early in the illness and perhaps explains why outbreaks in some countries were limited to only a few cases. More importantly it explains the poor sensitivity of early reverse transcriptase (RT)-PCR tests on nasopharyngeal (NP) specimens collected early in the illness. Although the main clinical symptoms are those of severe respiratory tract disease, the virus also infected other organs. About a quarter of SARS patients had a watery diarrhea. The virus can be cultured from the feces and urine as well as the respiratory tract. The virus also can be detected by RT-PCR in serum, plasma and peripheral blood leukocytes, however the viremia may be short lived. Disease severity and mortality was correlated with age, the highest mortality rates (52%) occurring in those >65 years of age and the lowest rate in the 0-24 year old group. Children acquiring SARS seldom required intensive care or mechanical ventilation. The SARS-CoV epidemic was controlled largely by a combination of strict infection control practices (including self quarantine in some cities) that was derived from well designed natural history studies. Early travel advisories from the WHO may have contributed to preventing or decreasing the importation of additional cases into industrialized countries. In two short years, SARS-CoV was identified, its genome sequenced, sensitive NAAT tests developed and subsequently effective vaccines developed for future use should the virus ever re-emerge. The fourth HCoV, named NL63, was first discovered in the Netherlands in a seven month old boy who presented with coryza, conjunctivitis, and fever. Chest X-ray findings were consistent with bronchiolitis (van der Hoek et al., 2004) . The virus grew in tertiary monkey kidney cells, which distinguished it from HCoV-OC43 and -229E. Sequencing the genome indicated that it was not a recombinant virus but genetically distinct from all other HCoVs. Following the first report, NL63 has been detected in hospitalized children in at least 8 countries around the world. The prevalence of infection has ranged from 1.2% to 9.3% but most often is between 1.5 and 3%. Children under the age of 5 were at highest risk of infection. Dual infections have been reported as high as 50% in one study in the Netherlands (van der Hoek et al., 2006) . Many of these studies were conducted in 2002-2003, and given that the distribution of CoVs may change from season to season, the relative frequency of CoVs may also change from year to year. In studies in the Netherlands, France, Switzerland, and Hong Kong where three or more CoVs were tested , it appears that NL63 was the most prevalent CoV detected in children (Chiu et al., 2005; Kaiser et al., 2005; Vabret et al., 2006; van der Hoek et al., 2006) . Whether NL63 continues to be the most frequently detected CoV in hospitalized children will have to await further seasonal studies. NL63 is predominantly a common cold virus like OC43 and 229E that can cause lower respiratory tract disease in young children, the elderly and immunocompromised patients. Recent studies from Germany and the Netherlands show that NL63 is associated with laryngotracheitis (croup) Konig et al., 2004; van der Hoek et al., 2006) . In one study, NL63 infection was associated with Kawasaki disease (Esper et al., 2005) . In this study 8 of 11 specimens from children with Kawasaki disease were positive for NL63 compared with only 1 of 22 control patients matched for age and time of sampling. Although this association was statistically significant the association has not been confirmed in three follow-up studies in Japan and Taiwan. Future studies with larger enrollments will be required to establish any association between NL63 and Kawasaki disease. The fifth HCoV, HKU1, was discovered in Hong Kong in a 71 year man returning from Shenzhen, China. He presented with fever and a productive cough with purulent sputum and had a chest radiograph showing patchy infiltrates. All attempts to grow a virus from NP specimens failed but coronavirus RNA was detected in an NPA specimen by RT-PCR using consensus PCR primers for the pol gene (Woo et al., 2005) . Quantitative PCR indicated high titers of virus (10 6 ) present in the NPA during the first week of illness with decreasing titers in the second week and undetectable levels of virus in the third and fourth weeks. HKU1 has now been identified in at least 9 countries on 4 continents and is worldwide in distribution. HKU1 causes both upper and lower tract infections. Prevalences of HKU1 have ranged from 1% to 11.3% but most studies indicate a range of 2−5%. Children <2 years of age are at highest risk of infection with HKU1. Coinfection rates with a second respiratory virus have been as high as 45% in one study (Kuypers et al., 2007) . It is most predominant in the autumn and winter months. The recent discovery over the past two years of three new HCoVs isolated from the upper respiratory tract of symptomatic patients suggests that additional as yet unidentified HCoVs may await discovery. Human bocavirus (HBoV) was discovered in Sweden in 2005. Since the first report by Allander et al. who reported a prevalence of 3.1% in hospitalized children with ARI, there are now studies from at least 12 countries in five continents, indicating that this virus is worldwide in distribution (Arnold et al., 2006; Kesebir et al., 2006; Manning et al., 2006) . HBoV has been associated with both upper and lower tract infections with prevalences ranging from 1% to 19%, with most reports indicating prevalences in the range of 3−6% in hospitalized children <5 years with ARI. Infections with HBoV are most prevalent in autumn and winter months in temperate climates in both the Northern and Southern hemispheres with few infections in summer months. HBoV infections have been detected in both children and adults but children under the age of two appear to be most at risk for infection. HBoV has been detected in children with abnormal chest radiographic findings in a several studies but the causative role of HBoV is not clear. Since HBoV is often detected together with a second respiratory virus (in one third to two thirds of cases) the question has been raised whether HBoV was the causative agent of respiratory tract disease. In a recent study HBoV was detected in children with acute wheezing with no other viruses present. This coupled with two recent studies indicating that HBoV is rarely detected in asymptomatic individuals (Kesebir et al., 2006; Manning et al., 2006) is strong evidence that HBoV is a causative agent of LRTI and in particular acute wheezing. Where the frequency of several different viruses was compared, HBoV was less common than RSV and Rhinovirus and approximately as common as influenza virus, human metapneumovirus, parainfluenza virus type 3, and adenoviruses and probably more common than coronaviruses and other parainfluenza viruses. The clinical significance of Mimivirus or Parv4 in respiratory illness has yet to be determined. Cloning of a human parvovirus by molecular screening of respiratory tract samples Human bocavirus: prevalence and clinical spectrum at a children's hospital Human coronavirus NL63 infection and other coronavirus infections in children hospitalized with acute respiratory disease in Hong Kong Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Prospective population-based study of viral lower respiratory tract infections in children under 3 years of age (the PRI.DE study) New DNA viruses identified in patients with acute viral infection syndrome Human coronavirus NL63 associated with lower respiratory tract symptoms in early life Antibody response in individuals infected with avian influenza A (H5N1) viruses and detection of anti-H5 antibody among household and social contacts Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus Prospective study of human metapneumovirus infection in children less than 3 years of age Clinical disease in children associated with newly described coronavirus subtypes Mimivirus in pneumonia patients Epidemiological profile and clinical associations of human bocavirus and other human parvoviruses Identification of severe acute respiratory syndrome in Canada Characterization of an avian influenza A (H5N1) virus isolated from a child with a fatal respiratory illness Probable person-to-person transmission of avian influenza A (H5N1) Detection of the new human coronavirus HKU1: a report of 6 cases A newly discovered human pneumovirus isolated from young children with respiratory tract disease Identification of a new human coronavirus Human coronavirus NL63 infection is associated with croup Summary of probable SARS cases with onset of illness from 1 Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia WFC: None declared. JBM: Stockholder, honoraria, patent applications (Luminex).