key: cord-0796361-zmodjaju
authors: Debiaggi, Maurizia; Canducci, Filippo; Ceresola, Elisa Rita; Clementi, Massimo
title: The role of infections and coinfections with newly identified and emerging respiratory viruses in children
date: 2012-10-27
journal: Virol J
DOI: 10.1186/1743-422x-9-247
sha: a63e10c460821fd20aa9f58b6d7f4634b05b16ce
doc_id: 796361
cord_uid: zmodjaju

Acute respiratory infections are a major cause of morbidity in children both in developed and developing countries. A wide range of respiratory viruses, including respiratory syncytial virus (RSV), influenza A and B viruses, parainfluenza viruses (PIVs), adenovirus, rhinovirus (HRV), have repeatedly been detected in acute lower respiratory tract infections (LRTI) in children in the past decades. However, in the last ten years thanks to progress in molecular technologies, newly discovered viruses have been identified including human Metapneumovirus (hMPV), coronaviruses NL63 (HcoV-NL63) and HKU1 (HcoV-HKU1), human Bocavirus (HBoV), new enterovirus (HEV), parechovirus (HpeV) and rhinovirus (HRV) strains, polyomaviruses WU (WUPyV) and KI (KIPyV) and the pandemic H1N1v influenza A virus. These discoveries have heavily modified previous knowledge on respiratory infections mainly highlighting that pediatric population is exposed to a variety of viruses with similar seasonal patterns. In this context establishing a causal link between a newly identified virus and the disease as well as an association between mixed infections and an increase in disease severity can be challenging. This review will present an overview of newly recognized as well as the main emerging respiratory viruses and seek to focus on the their contribution to infection and co-infection in LRTIs in childhood.

In the last decade thanks to progress in molecular technologies, newly discovered viruses have been identified. In 2001 human Metapneumovirus (hMPV) was identified, followed by discoveries or emergence of other respiratory viruses or virus strains: coronaviruses NL63 (HcoV-NL63) and HKU1 (HcoV-HKU1), human Bocavirus (HBoV), new enterovirus (HEV), parechovirus (HpeV) and rhinovirus (HRV) strains, polyomaviruses WU (WUPyV) and KI (KIPyV) and the pandemic H1N1v influenza A virus [1] [2] [3] [4] [5] [6] [7] [8] .

These discoveries have heavily modified previous knowledge on respiratory infections and have now highlighted that although until recently most viral lower respiratory infections in infants and young children were attributed to respiratory syncytial virus (RSV), PIVs, adenovirus, HRV and influenza viruses, pediatric population is indeed exposed to a variety of other viruses with a similar seasonal pattern [9] [10] [11] . In this context, establishing a causal link between a newly identified virus and the disease as well as an association between mixed infections and an increase in disease severity can be challenging. This review will present a brief overview of newly recognized as well as the main emerging respiratory viruses and seek to focus on the their contribution to infection and co-infection in LRTIs in childhood.

Metapneumovirus was first recognized in 2001 in the Netherlands from nasopharyngeal aspirates collected during a 20-year period in 28 hospitalized children and infants with acute respiratory tract infection (RTI) having signs and symptoms similar to that of RSV infection [4] . The virus genomic sequence was identified by using a randomly primed PCR protocol and revealed to be closely related to the avian pneumovirus, a member of the Metapneumovirus genus, in the Paramixoviridae family, Initial studies following the first hMPV identification indicate that it causes upper and lower RTIs in patients of all ages, but mostly in children aged below 5 years [12] [13] [14] [15] [16] [17] . A large epidemiological retrospective study examined nasal washes collected over a 20-year period during acute respiratory illnesses in an outpatient cohort of children [18] . Over the entire study period, hMPV was detected in 1%-5% of pediatric upper RTIs (UTRIs), with variation from year to year. Several reports indicate that hMPV is a commonly identified cause of pediatric lower RTIs, and is second only to RSV as cause of bronchiolitis in early childhood [16, [19] [20] [21] [22] [23] [24] [25] . While bronchiolitis, is the most common presentation of hMPV illness, other reported syndromes have included asthma exacerbation, otitis media, flulike illness, and communityacquired pneumonia [12, 15, [26] [27] [28] [29] . Several studies have found hMPV -RSV co-infection rates of approximately 5-14% [30] [31] [32] [33] [34] . Nevertheless, in a study conducted in the Netherlands in children admitted to hospital for lower RTIs (LRTIs), no virus co-infection between RSV and hMPV was detected [35] . Different controversial reports suggest an association between RSV-hMPV coinfection and an increase in the disease severity or the absence of an association between dual infection and disease severity. Greensill and colleagues [36] reported a 70% rate of co-infection with hMPV in a cohort of infants with critical RSV bronchiolitis who required intensive care in the United Kingdom, suggesting that dual infection with RSV and hMPV may predispose for a more severe disease. In another study from the United Kingdom, hMPV and RSV co-infection was associated with increased disease severity and higher risk of admission to the pediatric intensive care unit [37] . Similar findings are supported by other studies suggesting that in young children, coinfections with RSV and hMPV are more severe than infections with either RSV or hMPV alone, requiring a longer hospitalization and supplemental oxygenation [38, 39] . However, such synergistic association has not been found in other population-based and case-control studies of hospitalized children [16, [33] [34] [35] [40] [41] [42] . In particular, two studies evaluated the epidemiology of hMPV coinfection in children with LRTI caused by RSV and demonstrated no hMPV and RSV co-infection in mechanically ventilated children suggesting that co-infection with hMPV is not associated with a more severe course of RSV-LRTI [35, 42] . In addition, in a prospective 2-year study in hospitalized infants with acute respiratory diseases, the role of RSV as a major respiratory pathogen was not influenced by the cocirculation of other emerging viral agents with similar seasonal distribution. In particular, RSV-hMPVs co-infections were significantly observed in less severe respiratory disease when compared to unique RSV infections [34] . The possible synergistic interaction between hMPV and the severe acute respiratory syndrome (SARS) coronavirus was also suggested during the 2003 SARS outbreak in Hong Kong and Canada [43, 44] . In one case report, in an infant with SARS CoV infection, fatal encephalitis was correlated with hMPV infection as hMPV RNA was detected postmortem in brain and lung tissue [26] . Nevertheless, in experimental studies performed in macaques, a synergy between hMPV and SARS was not confirmed [45] . In addition, infections of hMPV with respiratory viruses different from RSV, have also been occasionally reported but no sufficient data are available to discuss epidemiology or association with clinical disease presentation [34, 46, 47] (Table 1) .

Following the discovery of SARS-CoV, other human coronaviruses, HCoV-NL63 and HCoV-HKU1, were identified and recognized to be common causes of communityacquired respiratory infections.

HCoV-NL63, a member of the group I coronaviruses, was first detected in 2004 in the Netherlands from a child with bronchiolitis by using a new method for virus discovery based on the cDNA-amplified restriction fragment−length polymorphism technique (cDNA-AFLP) [3] .

HCoV-HKU1, a group II coronavirus, was first detected in Hong Kong in 2005 from an adult patient with chronic pulmonary disease [1] . All attempts to grow a virus from his respiratory secretions failed until recently [48] , but coronavirus RNA was initially detected by RT-PCR using pol gene consensus primers.

Like other coronaviruses, NL63 and HKU1 can also be detected in individuals of all ages, including elderly patients with fatal outcome [49] and those with underlying diseases of the respiratory tract [1] . However most frequently, the newly discovered coronaviruses are reported in 7 to 12-month old children with both upper and lower RTIs [34, [49] [50] [51] [52] [53] . In studies conducted in children hospitalized with RTIs in China, from 2.6% to 3.8% of patients were positive for HCoV-NL63 and, in addition to causing upper respiratory disease, HCoV-NL63 was found in croup, asthma exacerbation, febrile seizures, wheezing and high fever cases [54, 55] . The occurrence of co-infection with NL63 and other respiratory viruses, including other human coronaviruses, RSV, PIV, influenza A and B viruses and hMPV has been reported [34, [55] [56] [57] [58] . In a large study from Germany evaluating children under 3 years of age with LRTIs, most co-infections were with RSV-A, probably because of the high percentage of RSV-A infections and an overlap in seasonality. In addition, double infection of NL63 with RSV-B, and with PIV3 occurred in a minority of cases. HCoV-NL63 co-infection with RSV-A occurred predominantly in the hospitalised patients in contrast to HCoV-NL63 co-infections with PIV3 that were exclusively present in the outpatient group [59] .

Following the first identification, HKU1 was found in respiratory samples from elderly patients and children mainly with underlying diseases [1, 33, 52, 60] . The most common symptoms are rhinorrhea, fever, and abdominal breath sounds [33] , but pneumonia, bronchopneumonia, bronchiolitis, and acute asthma exacerbations were also described in children in China [61, 62] .

In a study aimed to evaluate the overall prevalence of 10 respiratory viruses in children with acute LRTIs in China from 2006 to 2009, 73.47% of the HCoV-HKU1 and HCoV-NL63-positive samples tested positive for at least one other virus, most commonly HRV and RSV [54] . Similar data describing a high rate of coinfection of coronaviruses with RSV has also been previously reported [63] . In a report from the UK both dual and single infections associated with respiratory outcomes were observed for HKU1 as well as for NL63 and OC43 coronaviruses [51] . In this study a high number of coinfections was observed for HKU1, NL63 as well as for OC43, mostly with RSV. Similar rates of lower and upper infections were observed in single HKU1 or OC43 infection compared with coinfection, whereas both URTI and LRTI were observed more frequently in single compared to mixed infection with NL63. No differences in clinical outcome were observed between single and dual infections with RSV and Coronaviruses NL63, HKU1 or OC43 indicating that RSV may presumably facilitate coronavirus infection without increasing disease severity. However, in the same study considering viral load data, a role of these coronaviruses in coinfections in respiratory disease was suggested. In fact no differences were observed when coronavirus load was evaluated in single infection and in RSV coinfection, indicating both that infection with another respiratory virus does not affect the ability of NL63, HKU1 or OC43 to establish infection and replicate, and that detection of coronaviruses in mixed infection should not be considered a secondary infection without contribution to disease pathogenesis [51] . This quantitative evaluation is in contrast with previous results obtained by van der Hoek and colleagues describing a significantly lower HCoV-NL63 viral load in patients coinfected with RSV or PIV3 than in patients infected with HCoV-NL63 alone [59] . However, the prolonged persistence of HCoV-NL63 at low levels, the different time of sampling relative to the time of disease onset, or the use of different diagnostic technologies could have affected these evaluations (Table 1) .

Human Bocavirus (HBoV) was discovered in 2005, in Sweden by Allander and colleagues by using a largescale molecular viral screening technique including DNase sequence-independent single-primer amplification [6] . Since initial observations, several studies have reported the prevalence of human Bocavirus infection all over the world ranging from 2 to 21.5%, mainly in children younger than 3 years of age where it has been associated with upper and with lower RTIs [64] [65] [66] [67] [68] [69] . In a study from Norway, HBoV was detected in 12% of children with RTI and it was the fourth most common virus after RSV, HRV and hMPV [70] . Recently, in children with radiographically confirmed community acquired pneumonia in which 17 respiratory viruses were tested during the acute phase of the disease, HBoV was the most frequently detected virus after RSV and HRV [71] . Since the discovery of the first HBoV (HBoV1), three other related bocaviruses (HBoV2, 3 and 4) have been identified in stool samples and associated with gastrointestinal diseases [72, 73] . Serological studies on HBoV1 are in line with molecular data.

Serological studies have shown that the mere presence of HBoV DNA in the respiratory tract is not proof of an acute primary infection [65, [74] [75] [76] . These data are also supported by studies on consecutive respiratory samples showing that HBoV DNA can persist for several months in the respiratory tract [77] [78] [79] . Prolonged viral shedding could explain both data reported in some papers in which HBoV DNA was found more often in asymptomatic than symptomatic cases [79, 80] and the high percentage of co-infections. In fact, HBoV infections tend to be associated with high rates of coinfections with other viral pathogens such as HRV, adenoviruses, RSV, as well as with bacteria such as Streptococcus spp and Mycoplasma pneumoniae [46, 54, [68] [69] [70] 77, [81] [82] [83] . Characteristics of persistence and high frequency of coinfections have led to a debate over its role as a true pathogen [84] . Our current knowledge of HBoV infection suggests that the virus is sometimes a passenger and sometimes a pathogen in acute respiratory tract disease and that diagnosis should not be solely based on qualitative PCR in respiratory samples. Indeed, in many studies a positive correlation was seen between respiratory illness and high copy numbers of HBoV1 DNA or the presence of HBoV1 monoinfection [68, 75, [85] [86] [87] . A study performed by Allander and colleagues suggests that acute HBoV infections are associated with the presence of viral DNA in the blood of patients. In fact, HBoV DNA was reported more frequently in patient blood during the acute symptoms than after recovery [68] . In addition, high load and viremic HBoV infection were associated with respiratory tract symptoms, while detection of a low viral load in the nasopharinx alone resulted to have no clinical relevance [68] . Other studies confirmed that HBoV is the most probable cause of respiratory tract disease if the patient has a single infection and high viral load in NPA and viremia [65, 70] . However, despite these diagnostic challenges it is becoming increasingly evident that HBoV1 is an important respiratory pathogen [88] . Severe and life-threatening disease has been recently well documented in a 8-month-old Table 1 Recent epidemiological papers on respiratory infections and co-infections Table 1 Recent epidemiological papers on respiratory infections and co-infections (Continued)

co-infections were with RSV-A HCoV-NL63 co-infection with RSV-A occurred mainly in hospitalised patients in contrast to HCoV-NL63 co-infections with PIV3 that were exclusively present in the outpatient group. Lower HCoV-NL63 viral load in patients coinfected with RSV or PIV3 than in patients infected with HCoV-NL63 alone The prevalence of HboV was the second (11%), the first was RSV (23%). Among HBoV infections, a high rate (38%) was coinfection.

, (e) 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing

Acute HBoV infections appears associated with presence of viral DNA in the blood as the HBoV DNA was reported more prevalent in the patients blood during the acute symptoms than after recovery. High load and viremic HBoV infection were associated with respiratory tract symptoms, while detection of a low viral load in the nasopharinx alone has uncertain relevance

HBoV was detected in 12% of samples. It was the fourth most common virus in the material The prevalence of HBoV infection was 3.8%. HBoV. Viral load appears to be linked to the severity of the disease. child with acute respiratory distress attending an emergency department in Germany [89] . Don et colleagues [76] found serological evidence of an acute HBoV infection in 12% of children with pneumonia and in more than half of these cases with single HBoV infection. In most cases a significant rise in IgG antibodies between paired sera was found in children admitted to hospital for radiologically confirmed pneumonia. IgM antibodies were also detected in all but one patient. This study suggests that HBoV may be a fairly common cause of pneumonia in children Table 1 .

Two new polyomaviruses were identified in 2007 in respiratory tract samples following large scale molecular screening using high throughput DNA sequencing of random clones [5, 7] and have been named after the institutes where they were found: KI (Karolinska Institute) [90, 91] . Since their first identification, KI and WU viral sequences have been confirmed worldwide in respiratory samples from children with respiratory tract disease ranging from 0.2% to 2.7% and from 1.1 to 7%, respectively [91] [92] [93] [94] [95] [96] [97] . However WUPyV and KIPyV were found at similar frequencies in control groups without respiratory diseases so the link between these polyomaviruses and acute respiratory diseases remains speculative [94, 96, 98] . Careful analysis is complicated by high co-infection rates with other well-characterized viral respiratory pathogens. A co-detection rate of 74% has been observed for KIPyV and rates ranging from 68 to 79% for WUPyV [94, 95, 97] . Therefore, in a recent study in Southern China, hospitalized children with WUPyV infection displayed predominantly cough, moderate fever, and wheezing, but were also diagnosed with pneumonia, bronchiolitis, upper respiratory tract infections and bronchitis. As in most of infected children a single WUPyV infection was detected, it was suggested that the newly described polyomavirus can cause acute respiratory tract infection with atypical symptoms, including severe complications [99] . Nevertheless these data have to be confirmed in further studies.

The presence of WUPyV and KIPyV in samples from children but not from immunocompetent adults suffering from LRTIs suggests that these viruses primarily infect the young population [100] . A correlation between immunosuppression and reactivation of the two novel polyomaviruses has been suggested in immunocompromised patients [101] and in AIDS patients at the molecular level [102] , but no evidence of a role of these viruses as opportunistic pathogens has been given.

Overall, these data support the hypothesis that, in analogy with BK and JC polyomaviruses, KIPyV and WUPyV can establish persistent infection, and that virus replication may increase in immunocompromised hosts. However, in a recent study on immunocompetent and immunocompromised adult patients, real-time PCR detected KIPyV and WUPyV in 2.6% and 4.6% of HIV-1-infected patients respectively and in 3.1% and 0.8% of blood donors respectively, while no association was found between CD4+ cell counts in HIV-1 positive patients and infection with KIPyV or WUPyV [103] .

KIPyV and WUPyV are also incidentally detected in adults with community acquired pneumonia, in immunocompromised hosts, and in patients with lung cancer; they are more often found in patients suffering an underlying medical condition and coinfections with KIPyV and WUPyV with other respiratory viruses are common [92, 103, 104] . A recent study evaluating the prevalence and viral load of WUPyV and KIPyV in respiratory samples from immunocompromised and immunocompetent children showed that the prevalence of WUPyV and KIPyV is similar in hematology/oncology patients compared with that of the general pediatric population [105] . High co-detection rates with other respiratory viruses, mainly RSV and enterovirus or rhinovirus, were found for WUPyV and KIPyV in both groups, in analogy with previous reports. However, higher viral loads for KIPyV in the immunocompromised group were detected, suggesting that there may be an increased replication of this virus in this population.

A similar association was not observed for WUPyV. Furthermore, in the immunocompromised group, infection with either virus occurred in older children compared with controls, which may indicate viral-reactivation Table 1 .

HRVs are currently classified in the Picornaviridae family, genus Enterovirus, that includes 3 species: HRV-A, HRV-B, and HRV-C. Within each species there are multiple HRVs designated as "serotypes", "types", or "strains". Several recent epidemiological studies suggest that HRV-A and HRV-C are the predominant species associated with acute respiratory illnesses in hospitalized children and adults, compared to HRV-B which are rarely detected [106] .

The new HRV lineage designated HRV-C has been identified using molecular methods and associated with severe clinical presentations in infants and immunocompromised adults. Symptoms of patients infected with this new strain were mainly bronchiolitis, wheezing, and asthmatic exacerbation in cases from Australia and Hong Kong, which peaked in fall and winter whereas in New York the new rhinovirus genotype was detected in cases of influenza like illness (ILI) that were clustered within an 8-week period from October to December [62, 107, 108] . A recent study describes a clinical case of severe respiratory and pericardial disease in an infant infected by HRV-C suggesting tha viral tropism is not strictly restricted to the respiratory tract [109] . A study focusing on the global distribution of novel rhinovirus indicates its association with community outbreaks and pediatric respiratory disease also in Africa and in symptomatic subjects living in remote locations having limited contacts with other human populations. Moreover evidence for a role of HRV-C in lower respiratory tract disease and febrile wheeze in infants and asthma exacerbations in older children was reported [110] [111] [112] [113] [114] . Recent studies making comparisons between HRVs species, found the HRV Cs more so than As or Bs as the major contributors to febrile wheeze and asthma exacerbation in infants and children, respectively . However, the severity of clinical manifestations for HRV-C is comparable to that for HRV-A in children with communityacquired pneumonia [115] . In HRV C studies so far, no clear clinical difference has been noted between patients with single or mixed HRV-C infection [111, 113, 116] . In a study, monoinfection was observed in more than half of cases and was more common than RSV monoinfection in patients with upper RTD, however the duration of hospitalizations was not significantly different between the HRV-C monoinfection group, HRV-A or HRV-B monoinfection group and RSV group suggesting that HRV-C is an important etiological factor in children with RTI [117] .

Most HRV-C co-detections are with RSV [113, [117] [118] [119] , however in a large study HRVs were statistically the least likely virus of 17 examined to be associated with coinfections [120] Table 1 .

A novel HEV (EV104) genotype was first identified in Switzerland in 2010 from respiratory samples collected during 2004-2007 in 8 children with respiratory signs and symptoms and acute otitis media [121] . In a following epidemiologic study conducted in Italy, five strains of the new EV104 genotype were detected in patients with respiratory diseases [122] . Patients were aged 2 to 62 years and most had underlying diseases; in immunocompetent patients EV104 was associated with chronic rhinopharyngytis, whereas in immunocompromised patients with symptoms of acute respiratory tract infection including wheezing, fever and rhinorrhea. Only in one out of 5 patients a coinfecting virus was detected.

EV109 was first discovered from a case of acute respiratory illness in a Nicaraguan child in September 2010; EV109 isolates were then detected in 1.6% of respiratory samples of children with influenza like illness (ILI) in Managua, and recognized to have a pathogenetic role in the illness [2] . After this characterization, a species C of HEV distantly related to EV109 was retrieved from a rectal swab of a deceased patient during an outbreak of flaccid paralysis in Congo; in this sample poliovirus and other neurologic, enteric and respiratory viral pathogens were not detected [123] . The global distribution of EV 109 is currently unknown and only a few studies have been performed yet to evaluate epidemiological features of this infection. [124, 125] To date the pathogenic role of these new enterovirus strains has still to be defined in larger clinical and epidemiological surveys Table 1 .

There are fourteen known HPeV genotypes that were isolated mainly in young children [126] [127] [128] [129] [130] [131] [132] [133] [134] Two recent studies have investigated the involvement of HPeVs in respiratory diseases reporting a low frequency of detection and a lack of clear disease association [135, 136] . Both studies detected HPeV infections mostly in children below 5 years and the most commonly identified parechoviruses were HPeV1 and HPeV3, while HPeV4, HPeV 5 and HPeV 6 were detected in a minority of cases. However, in addition to a low HPeVs prevalence in respiratory samples, a high rate of co-infection with other respiratory viruses was observed in HPeV positive samples, making it difficult to define a pathogenic role of these new HPeV genotypes in child respiratory infections.

In March 2009, a novel reassortant influenza strain (A/ H1N1v) was discovered in Mexico as an infective agent in humans [137, 138] . From April 15 through May 5, 2009, a total of 642 confirmed cases of human infection with the outbreak strain of H1N1v were identified in 41 states in the USA [139, 140] . Of the patients with confirmed infection, 9% required hospitalization. The age of hospitalized patients ranged from 19 months to 51 years and among the hospitalized patients for whom data were available, 18% were children under the age of 5 years. Multiple reports have described the clinical features of infection with this novel virus, which are similar or milder to those of seasonal influenza, [141, 142] . The spectrum of clinical presentation varies from self limiting respiratory tract illness in most cases, to primary viral pneumonia resulting in respiratory failure, acute respiratory distress, multi-organ failure and death, most of them occurring in patients with underlying medical conditions [142] .

During the A/H1N1v flu wave, due mainly to the lack of cross-neutralizing anti-influenza antibodies [143, 144] or the presence of co-morbidities, more children and younger adults were infected by the pandemic flu strain and had serious disease than in the seasonal epidemic. For this reason they were identified as a particular risk group, together with pregnant women [145, 146] . Young children presented a higher attack rate than older adults and a greater mortality rate than previously observed with classical seasonal flu [147, 148] . In a study conducted in England from June 2009 to March 2010, a childhood mortality rate of 6 per million population was reported. The rate was highest for children less than 1 year and with severe pre-existing disorders [149] . Similar data are reported in other studies highlighting that most severe cases occurred in children with known comorbidities [150] [151] [152] [153] .

The occurrence of co-infection with influenza A H1N1v and other respiratory viruses has been reported in few studies. In a study conducted in France and aimed at investigating respiratory pathogens involved in ILI during the early weeks of the 2009-29010 H1N1v diffusion, 19% of samples positive for H1N1v were also positive for other respiratory pathogens. In mixed infections, HRV was the more frequent co-pathogen being detected in 13.2% of all samples positive for H1N1v [154] . However, HRV infections represented nearly half of non-H1N1v viral infections and the increase of H1N1v positive cases was associated with a rapid decline of HRV infections. In addition, the frequency of virus co-infection was slightly but not significantly higher in samples positive for H1N1v as compared with samples positive for other respiratory pathogens and viral mixed infection both with H1N1v and other viruses was not associated with a different clinical presentation. Similar co-infection data are reported in a prospective study evaluating a combination of two RT-PCR DNA microarray systems in virological routine diagnosis of ILI [155] . In both studies conducted in France, in the same H1N1v early pandemic period, few RSV infections were reported compared with epidemiological data in the same period of the last four years. The delayed and reduced circulation of RSV observed in 2009-10 compared with 2008-09 suggests that the early circulation of the 2009 pandemic influenza A(H1N1) viruses had an impact on the RSV epidemic [156] . A significant inverse relationship between HRV and A H1N1 pandemic virus was also reported, suggesting that the presence of HRV reduces the risk of infection by the H1N1 virus and thus, indirectly, the spread of the virus [156] Table 1 .

Torque tenovirus (TTV), is classified in the new genus Anellovirus [157] . TTV produces long-lasting (possibly life-long) viremia in about 80% of apparently healthy individuals of all ages and living in different countries [158] . Although no evidence was obtained that TTV is a direct cause of acute respiratory diseases, it was observed that average viral loads are considerably higher in children with bronchopneumonia than in children with milder illnesses, regardless of the presence of common respiratory viruses [159] . Further studies could not confirm the association, but documented a link between TTV infection in children and asthma, suggesting that TTV might be a contributing factor in the lung impairment caused by this condition [160] . Finally, it was documented that TTV is able to infect respiratory ciliated cells and that these cells are potentially able to support viral replication [161] . Far from being conclusive, the data suggest that these viruses may replicate efficiently in the respiratory tract of children with and without acute respiratory infections by other respiratory viruses, and that although TTV does not have a clear pathogenic role in acute respiratory diseases, it may influence the clinical presentation of the disease.

Over the past 10 years, advances in scientific knowledge and the availability of new technologies have deeply changed our views in the field of respiratory viral infections. In particular, the identification of new viruses or viral strains has allowed to better define the viral etiology in many respiratory diseases where the viral pathogen was only hypothesized or suspected.

Molecular virological diagnosis has thus gained an increasing importance with the development of novel molecular assays, in some cases able to detect many respiratory viruses simultaneously.

Nevertheless, despite the availability of novel diagnostic assays, data are still controversial regarding the role of coinfection in a more severe clinical outcome in comparison to single infections.

In this context, even though specific antiviral compounds or vaccines are being developed, the level of accuracy and the associated higher costs of complex molecular assays to highlight the presence of one or more viruses in the same samples, are often considered not to be clinically necessary.

However, some important considerations emphasize the importance of implementing diagnostic approaches that allow the identification of the greatest number of newly identified or emerging viral respiratory pathogens. Firstly, the use of diagnostic assays able to simultaneously detect more respiratory viruses, including the newly identified ones, and in some cases their load, will help to clarify virus-host interactions which are still partially unknown, in particular in hospitalized patients. This will allow to develop appropriate control measures for nosocomial infection containment. Moreover, in many cases respiratory viruses pave the way to severe secondary bacterial infections. Thus the rapid identification of viral pathogens may help to limit disease progression and to plan appropriate monitoring and patient management in defined clinical settings. Furthermore, rapid and reliable screening with large panel of respiratory viruses responsible for upper and lower RTIs is of major epidemiological and clinical interest for monitoring influenza pandemic waves or unexpected respiratory outbreaks.

In addition, in the case of emerging viral strains as well as for enteroviruses, parechovirus or rhinoviruses the subsequent or simultaneous circulation of genetically distinct strains with distinct pathogenic potential, suggests a high risk for repeated pediatric respiratory infections as well as the possibility of genetic recombination within species. In these cases, the continuous development of quantitative assays associated with viral genotyping assays will allow the rapid and valuable etiological diagnosis of enterovirus, parechovirus or rhinovirus childhood infections, helping to prevent both nosocomial transmission and to control the emergence of new respiratory strains with unpredictable pathogenic potential.

The authors declare that they have no competing interests.

Authors' contributions MD, FC, MC wrote the manuscript. ERC organized the table. All authors read and approved the final manuscript. 

Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia

Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua

Identification of a new human coronavirus

Osterhaus AD: A newly discovered human pneumovirus isolated from young children with respiratory tract disease

Identification of a third human polyomavirus

Cloning of a human parvovirus by molecular screening of respiratory tract samples

Identification of a novel polyomavirus from patients with acute respiratory tract infections

Detection of respiratory viruses by molecular methods

New respiratory viruses and the elderly

Emerging respiratory agents: new viruses for old diseases?

Respiratory viral infections in infants: causes, clinical symptoms, virology, and immunology

Metapneumovirus and acute wheezing in children

Human metapneumovirus infections in young and elderly adults

Human metapneumovirus as a cause of community-acquired respiratory illness

Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups

Human metapneumovirus infections in hospitalized children

Human metapneumovirus infections cause similar symptoms and clinical severity as respiratory syncytial virus infections

The role of human metapneumovirus in upper respiratory tract infections in children: a 20-year experience

Prevalence and clinical symptoms of human metapneumovirus infection in hospitalized patients

Prevalence of human metapneumovirus and influenza virus infections among Japanese children during two successive winters

Differential production of inflammatory cytokines in primary infection with human metapneumovirus and with other common respiratory viruses of infancy

Presence of the new human metapneumovirus in French children with bronchiolitis

Epidemiological survey of human metapneumovirus infection in a large pediatric tertiary care center

Epidemiology of human metapneumovirus

Human metapneumovirus-associated hospital admissions over five consecutive epidemic seasons: evidence for alternating circulation of different genotypes

Frequency of human metapneumovirus in the upper respiratory tract of children with symptoms of an acute otitis media

Detection of human metapneumovirus from children with acute otitis media

Human metapneumovirus infections in children

Management of community-acquired pneumonia in infants and children older than 3 months

Human Metapneumovirus as a causative agent of acute bronchiolitis in infants

High prevalence of human metapneumovirus infection in young children and genetic heterogeneity of the viral isolates

Human metapneumovirus and lower respiratory tract disease in otherwise healthy infants and children

Human metapneumovirus infection in the United States: clinical manifestations associated with a newly emerging respiratory infection in children

Two-year prospective study of single infections and co-infections by respiratory syncytial virus and viruses identified recently in infants with acute respiratory disease

Absence of human metapneumovirus co-infection in cases of severe respiratory syncytial virus infection

Human metapneumovirus in severe respiratory syncytial virus bronchiolitis

Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis

Human metapneumovirus infection in young children hospitalized with respiratory tract disease

Prospective study of human metapneumovirus infection in children less than 3 years of age

Human metapneumovirus associated with respiratory tract infections in a 3-year study of nasal swabs from infants in Italy

Comparison of human metapneumovirus, respiratory syncytial virus and influenza A virus lower respiratory tract infections in hospitalized young children

Human metapneumovirus and severity of respiratory syncytial virus disease

Identification of severe acute respiratory syndrome in Canada

Human metapneumovirus detection in patients with severe acute respiratory syndrome

Aetiology: Koch's postulates fulfilled for SARS virus

The association of newly identified respiratory viruses with lower respiratory tract infections in Korean children

Correlation of viral load of respiratory pathogens and co-infections with disease severity in children hospitalized for lower respiratory tract infection

Culturing the unculturable: human coronavirus HKU1 infects, replicates, and produces progeny virions in human ciliated airway epithelial cell cultures

Human coronavirus NL63 infection in Canada

The novel human coronaviruses NL63 and HKU1

Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method

Human coronavirus NL63, France. Emerg Infect Dis

Detection of human coronavirus NL63, human metapneumovirus and respiratory syncytial virus in children with respiratory tract infections in south-west Sweden

Newly identified respiratory viruses associated with acute lower respiratory tract infections in children in Lanzou

Human coronavirus NL63 infection and other coronavirus infections in children hospitalized with acute respiratory disease in Hong Kong

Phylogenetic analysis of human coronavirus NL63 circulating in Italy

Human coronavirus infections in rural Thailand: a comprehensive study using real-time reverse-transcription polymerase chain reaction assays

Clinical manifestations of human coronavirus NL63 infection in children in Taiwan

Croup is associated with the novel coronavirus NL63

Two cases of severe obstructive pneumonia associated with an HKU1-like coronavirus

Coronavirus HKU1 and other coronavirus infections in Hong Kong

Clinical disease in children associated with newly described coronavirus subtypes

Human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in Thailand

Clinical assessment and improved diagnosis of bocavirus-induced wheezing in children

Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus

Human bocavirus in Italian patients with respiratory diseases

Human bocavirus and acute wheezing in children

High prevalence of human bocavirus 1 in infants with lower acute respiratory tract disease in Argentina

Human bocavirus commonly involved in multiple viral airway infections

Impact of viral infections in children with community-acquired pneumonia: results of a study of 17 respiratory viruses

Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections

A novel bocavirus associated with acute gastroenteritis in Australian children

Serodiagnosis of human bocavirus infection

Dating of human bocavirus infection with protein-denaturing IgG-avidity assays-Secondary immune activations are ubiquitous in immunocompetent adults

Serologically verified human bocavirus pneumonia in children

Frequent and prolonged shedding of bocavirus in young children attending daycare

Prolonged detection of human bocavirus DNA in nasopharyngeal aspirates of children with respiratory tract disease

Clinical and epidemiologic characteristics of human bocavirus in Danish infants: results from a prospective birth cohort study

Human bocavirus infections in hospitalized children and adults

Epidemiological profile and clinical associations of human bocavirus and other human parvoviruses

Clinical characteristics of human bocavirus infections compared with other respiratory viruses in Spanish children

Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China

Human bocavirus: passenger or pathogen in acute respiratory tract infections?

Correlation between bocavirus infection and humoral response, and co-infection with other respiratory viruses in children with acute respiratory infection

The human bocavirus role in acute respiratory tract infections of pediatric patients as defined by viral load quantification

Development of duplex real-time PCR for detection of two DNA respiratory viruses

Human bocavirus-the first 5 years

Severe human bocavirus infection

Seroepidemiology of human polyomaviruses

High prevalence of antibodies against polyomavirus WU, polyomavirus KI, and human bocavirus in German blood donors

Molecular epidemiology of KI and WU polyomaviruses in infants with acute respiratory disease and in adult hematopoietic stem cell transplant recipients

Agerelated pattern of KI and WU polyomavirus infection

WU polyomavirus in children with acute lower respiratory tract infections

Clinical and epidemiologic characterization of WU polyomavirus infection

WU polyomavirus in children

Presence of the newly discovered human polyomaviruses KI and WU in Australian patients with acute respiratory tract infection

No evidence for an association between infections with WU and KI polyomaviruses and respiratory disease

WU polyomavirus infection among children in South China

WU and KI polyomavirus present in the respiratory tract of children, but not in immunocompetent adults

Polyomaviruses KI and WU in immunocompromised patients with respiratory disease

Reactivation and mutation of newly discovered WU, KI, and Merkel cell carcinoma polyomaviruses in immunosuppressed individuals

KI and WU polyomaviruses and CD4+ cell counts in HIV-1-infected patients

Human polyomavirus KI and WU in adults with community acquired pneumonia in The Netherlands

Simoes EA: WU and KI polyomavirus infections in pediatric hematology/oncology patients with acute respiratory tract illness

Clinical and molecular features of human rhinovirus C

MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness

Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis

Pneumonia and pericarditis in a child with HRV-C infection: a case report

Newly identified human rhinoviruses: molecular methods heat up the cold viruses

Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children

Novel human rhinoviruses and exacerbation of asthma in children

A novel group of rhinoviruses is associated with asthma hospitalizations

Genetics, recombination and clinical features of human rhinovirus species C (HRV-C) infections; interactions of HRV-C with other respiratory viruses

Human rhinovirus C infections mirror those of human rhinovirus A in children with community-acquired pneumonia

Rhinovirus associated with severe lower respiratory tract infections in children

Prevalence and clinical characterization of a newly identified human rhinovirus C species in children with acute respiratory tract infections

Human rhinovirus group C infection in children with lower respiratory tract infection

High prevalence of human rhinovirus C infection in Thai children with acute lower respiratory tract disease

Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections?

New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses. Emerg Infect Dis

Enterovirus genotype EV-104 in humans

Type 1 wild poliovirus and putative enterovirus 109 in an outbreak of acute flaccid paralysis in Congo

Epidemiological, molecular and clinical features of Enterovirus 109 infection in children and in adult stem cell transplant recipients

Human enterovirus 109 (EV109) in acute paediatric respiratory disease in Hungary

Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains

Human parechovirus infections in Dutch children and the association between serotype and disease severity

Isolation and identification of a novel human parechovirus

Isolation and characterization of novel human parechovirus from clinical samples

Human parechovirus 3 and neonatal infections

Novel human parechovirus

Novel human parechovirus from Brazil

Recombination dynamics of human parechoviruses: investigation of type-specific differences in frequency and epidemiological correlates

Genomic characterization of novel human parechovirus type

Epidemiology and clinical associations of human parechovirus respiratory infections

Human parechovirus infections in patients admitted to hospital in Northern Italy

Borja-Aburto VH: Infection and death from influenza A H1N1 virus in Mexico: a retrospective analysis

On the spread of the novel influenza A (H1N1) virus in Mexico

Emergence of a novel swine-origin influenza A virus (S-OIV) H1N1 virus in humans

Emergence of a novel swine-origin influenza A (H1N1) virus in humans

Pneumonia and respiratory failure from swine-origin influenza A (H1N1) in Mexico

Hospitalized patients with 2009 H1N1 influenza in the United States

Monoclonal antibodies isolated from human B cells neutralize a broad range of H1 subtype influenza A viruses including swine-origin Influenza virus (S-OIV)

Molecular cloning of the first human monoclonal antibodies neutralizing with high potency swine-origin influenza A pandemic virus (S-OIV)

Pregnancy and H1N1 infection

Pediatric hospitalizations associated with 2009 pandemic influenza A (H1N1) in Argentina

Incidence of 2009 pandemic influenza A H1N1 infection in England: a cross-sectional serological study

Paediatric mortality related to pandemic influenza A H1N1 infection in England: an observational populationbased study

Hospitalized patients with 2009 pandemic influenza A (H1N1) virus infection in the United States

Swine-origin influenza virus H1N1, seasonal influenza virus, and critical illness in children

Children hospitalized with 2009 novel influenza A(H1N1) in California

Novel influenza A(H1N1) in a pediatric health care facility in New York City during the first wave of the 2009 pandemic

High burden of noninfluenza viruses in influenza-like illness in the early weeks of H1N1v epidemic in France

Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcription-PCR DNA microarray systems

Rhinoviruses delayed the circulation of the pandemic influenza A (H1N1) 2009 virus in France

TTV, a new human virus with single stranded circular DNA genome

Molecular properties, biology, and clinical implications of TT virus, a recently identified widespread infectious agent of humans

TT virus in the nasal secretions of children with acute respiratory diseases: relations to viremia and disease severity

Associations between nasal torquetenovirus load and spirometric indices in children with asthma

Torquetenovirus infection and ciliary dysmotility in children with recurrent pneumonia

Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution