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Within the etiology of acute respiratory infections (ARIs), viruses play an important role and they are the main cause of ARIs in children under the age of five and, in some cases, they also become an important cause of death. Usually, the human respiratory tract is attacked by pathogens such as influenza A and B viruses, respiratory syncytial virus (RSV), adenoviruses, and parainfluenza 1, 2, and 3 viruses, and most recently, other pathogens such as human metapneumovirus (hMPV) and rhinovirus have been detected.[4, 5] The RSV was reported as the main etiologic agent for ARIs in children under the age of one.
Some of these agents prefer certain age groups, as RSV and rhinovirus affect mainly children under the age of one; however, they can be found at any age depending on the host's immune status. Children are very vulnerable to ARIs because of their immune system immaturity, associated with very close interpersonal contact (in day cares and schools) and many times in settings without proper protection measures such as frequent hand-washing, vaccination, and others. Chronic pathologies such as Down syndrome, cystic fibrosis, and bronchopulmonary dysplasia also favor respiratory infections.[8, 9]
Upper respiratory infections usually present a non-specific spectrum of clinical manifestations, which hinders the correct identification of bacterial or viral infections and leads treating physicians to prescribe unnecessary antibiotics. The timely etiological diagnosis allows clinicians to properly administer drugs and implement epidemiologic measures.[10, 11]
In Colombia, the lack of published data regarding etiologic agents and burden of respiratory disease, in particular influenza-like illness (ILI), is notable. Few studies have found the causes, frequency, and symptoms of respiratory viral infections in children, its mortality, and the potential association with peak seasons of influenza,[12-14] and most of these studies have been fairly specific, developed in a short period of time and with a small sample size. A sentinel surveillance system established in Bogota and Manizales by the National Institute of Health of Colombia has shown that RSV was the most frequent agent in children under the age of five enrolled once a week in the emergency room and the daily medical consultation. Although adenovirus cases were rare, they were usually more severe.[15, 16]
Circulating strains of RSV and hMPV from South America (including Colombian samples) were recently genetically analyzed.[17, 18] Also recently, the first six cases of hMPV were reported in Medellin, Colombia.
As part of an ongoing collaboration among the Universidad de Antioquia in Medellin along with its Immunovirology Group, the Hospital Pablo Tobón Uribe (HPTU), and US Naval Medical Research Unit No 6 (NAMRU-6), based in Lima, Peru, an epidemiologic surveillance for influenza and other respiratory viruses in Medellin, Colombia, was conducted. It described the influenza strains that were circulating in the region along with their distribution over time and performing molecular characterization to some of those strains. This will contribute to the knowledge of local (Medellin and its metropolitan area) and national (Colombia) epidemiology, as well as that of the South American region. This epidemiologic surveillance network has previously described influenza and other respiratory virus circulation in other countries.[20-23] The aim of our study was to show the clinical–epidemiologic and phylogenetic characteristics of circulating respiratory viruses in Medellin, Colombia.
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- Materials and methods
- Funding statement
- Conflict of interest
- Copyright statement
Prior to this study, there was a paucity of published data about respiratory infections, in Medellin. Other comparable studies use tests such as immunofluorescence or immunoenzymatic assays, whereas this study uses viral cultures and/or RT-PCR for diagnostic confirmation. The duration of the study and the significant number of samples collected will help local physicians and epidemiologists to understand the clinical and epidemiologic characteristics of viral respiratory infections in a high complexity hospital of Medellin. However, as this study was conducted as a permanent surveillance of ILIs in one hospital, data cannot be generalized to the Colombian population, including that of Medellin.
Usually in Colombia, viral ARI diagnosis is based upon clinical data and immunofluorescence or immunoenzymatic assays for respiratory viruses. The Instituto Nacional de Salud of Bogota is the only one that uses RT-PCR for influenza diagnosis. This study found viral agents undetected before such as human metapneumovirus, a viral pathogen first reported in Colombia by our group. Using three different cell lines for isolation addressed the potential lack of local viral isolation capabilities also. This should contribute to broadening the physician's view on viruses associated with respiratory tract infections.
Clinical symptoms normally do not allow for distinguishing the agents causing ARIs; however, some clinical manifestations are more characteristic in certain types of viruses, such as bronchiolitis and RSV infection. Cough, malaise, and rhinorrhea are the main symptoms among ARI patients; nevertheless, these symptoms are not characteristic of a certain pathogen agent. Some clinical manifestations are more frequent in children and not so common among adults, such as manifestations in the digestive tract (diarrhea, vomits, and abdominal pain); in our case, vomits (15·6%) were the most frequent digestive manifestation among children.
During this surveillance system, samples were collected throughout the year as a reflection of the occurrence of medical visits based on respiratory diseases in general Medellin population, although there was a peak of visits in 2009, very likely because of the influenza A/pH1N1 pandemic emergence in April 2009. Besides, in 2009 and 2010, the winter season caused by La Niña phenomenon in Colombia had major rainfalls compared with reports from other years.
This study focused on ILI cases, and although 69% of our population was under the age of five, only a small number of RSV cases (2·4%) were reported. RSV is an extremely labile virus, and even though our samples were kept frozen at −70°C from collection to processing in Lima, Peru, this aspect plus time-related issues between collection and processing likely resulted in the small number of cases in this report. It has also been demonstrated previously that immunofluorescence on cultured cells is not the best technique for RSV detection.[29-31] In Argentina, for instance, immunofluorescence was used to identify RSV in a pediatric population (27%), because it is one of the most common viruses found among children. Even in young children with bronchiolitis, RSV was the most common virus, detected in 77% of patients.
This study clearly shows (Figure 2) that during the first year of life, non-influenza viral agents are predominant (approximately 70%), which changes as one gets older. Between one and 4 years of age, both influenza and non-influenza cases represent 50%. From five years to fourteen, and during young adulthood, the percentage of influenza cases predominate (70%). For all other age ranges, non-influenza viruses again become more frequent, as is the case of RSV and parainfluenza.
As far as influenza A and B viruses, though detected at a very early age, most cases occurred in children aged between 5 and 10, as published elsewhere, whereby school children are the main target of the viral infection and disseminators at home and school. In our study, 276 (37·4%) of positive cases were influenza A and 150 (20·4%) were influenza B, which highlights the importance of these viruses in the genesis of local respiratory infections.
The finding of a most affected population (school children) would also be useful to implement epidemiologic measures in the population, that is, intensifying vaccination in these age groups to try to control epidemics, without neglecting higher risk groups. Following influenza, adenovirus was found in 141 (19·1%) of positive cases, and although they were present throughout the period of the study, there was a significant increase in cases between September and December only in 2007 and 2010. During the study period, the case distribution fails to present defined seasonality (Figure 1). In 2010, this overlapped an adenovirus outbreak reported in Bogota by health authorities during the same period (unpublished). Adenoviruses became a very important cause of ILI in our study, especially among children under the age of five, as published elsewhere.
During all 6 years of study, influenza A virus circulated almost throughout the year. Only three clearly defined influenza B circulation periods were observed, in 2008, 2010, and 2012. This suggests that influenza B has a biannual circulation in the metropolitan area of Medellin. Most cases occurred between April and August toward the end of the first rainy season and during dry season or summer. In other publications of the Latin American region such as Ecuador, Venezuela, and Peru, this biannual pattern is not clearly defined and influenza A and B viruses can be found in almost all years reported.[20, 22, 23]
The MoH in Colombia has decided to use the southern hemisphere influenza vaccine, considering the circulation of strains around the region. So, the influenza vaccination campaign starts at the beginning of each year and extends through the rest of it depending on the vaccine availability. Privilege is granted to populations at risk, such as subjects older than the age of 60, pregnant women, small children, and subjects with a basal illness.
As far as frequency, after influenza A and B and adenovirus, parainfluenza viruses follow and circulate all year round, but if virus types are analyzed as a whole, most of them appear in the first semester of the year and overlap the first winter season and the most affected group is that of children under the age of five, as reported elsewhere. Adenovirus being most associated with a coinfection is also interesting; however, in other studies,[22, 35, 36] other viruses were more frequent found in coinfections, reason for which this piece of information may not be epidemiologically significant, yet it may be clinically important if we consider adenoviruses may produce severe clinical manifestations that can worsen those caused by another coinfection-associated virus; however, several studies do not report any difference in severity. In this study, it was associated with influenza A, influenza B, parainfluenza 1, HSV, and hMPV in the coinfection. The presence of coinfections with one or more viral agents has been reported quite frequently in the literature, but the clinical and epidemiologic significance is yet to be determined. These coinfections can benefit from the fact that patients may have basal diseases that favor both viral colonization and bacterial colonization. When several viral agents circulate simultaneously, the following can happen: an individual can get infected by two or more of them, though that it is not what “normally” occurs. A question that also comes up in the case of co infections is which of the two or more viral agents is producing the clinical manifestations mainly: Is it adenovirus or the associated virus? Yet, there are asymptomatic or mild cases among viral respiratory infections, and thus, it is difficult to elucidate what the contribution of each virus to the clinical manifestation is.
Parainfluenza viruses 1–3 are human pathogens that are more frequent than parainfluenza 4, as reported by the literature. We only found two cases of parainfluenza four during the study. Other parainfluenza viruses circulated sporadically, simultaneously, and in low proportion with respect to the cases. However, all virus types were detected mostly in children under the age of five, especially in those under the age of two. It is known that other viral agents may affect the respiratory tract although this is not its main target organ. Such is the case of enterovirus and herpes simplex, but as found in our study when they were the only isolated agent, we should think they are the ones causing ILI. Nevertheless, as expected, its frequency is very low and other characteristics of the patient may have influenced to favor this infection.
Medellin is a city with tropical climate where the seasons are not clearly defined; rather, there are seasons of rainfall and lack of rainfall, which locally are called winter and summer. We definitely found lack of clear seasonal trends for any of the respiratory pathogens.
One objective of this study was to identify the circulating influenza strains helping the evaluation of current vaccine components and inform of the composition of the future vaccine. Influenza vaccination was massive in many countries after the 2009 pandemic, and in Colombia, the southern vaccine was mainly used. However, our phylogenetic trees show that for serotypes B and A/H3N2, different strains have circulated simultaneously in Colombia, and both, northern hemisphere and southern hemisphere strains, were observed. This situation is not seen with subtype A/H1N1pdm09 because since its appearance in 2009, the strain has remained similar and changes have happened worldwide quite rapidly. These findings raise the importance of a closer observation of circulating strains to select the most effective vaccine for this country.
More importantly, in the case of A/H3N2 strains, our genetic analyses revealed that some 2008 and 2009 strains found by our system do not group with the recommended vaccine strain for those years and suggest that the vaccine could not have been protective against those circulating strains. We found isolations from 2010 to 2012 grouped with the selected vaccine strains Perth/16/2009 and Victoria 361/2011. Then, patients who got any of the influenza strains analyzed in 2010–2011 could have been protected by the yearly vaccine. On the other hand, some strains from 2008 and one from 2009 grouped to Perth/16/2009 as well, but Perth was not the selected vaccine those years. Many strains from 2007 grouped to Brisbane/10/2007 suggesting that in 2007 the vaccine was protective. It could be said that the California strain from 2007 was replaced by the Perth strain in 2008 and this trend is ongoing.
In contrast to the genetic diversity observed on A/H3N2 viruses, the phylogenetic analysis of some influenza strains isolated during the study period showed that A/pH1N1 strains grouped to both California 7/09 and 2009 pandemic Mexico strains. Other strains from 2007 to 2008 grouped to the seasonal strain, Brisbane, as expected. This suggests that the vaccine was protective against the circulating strains in all those years. Our system only found 02 samples positive for influenza H1N1pdm09 in 2012. As far as influenza B strains, the phylogenetic analysis showed that samples analyzed from 2010 to 2012 grouped to Brisbane/60/2008 strain, which corresponds to the period vaccine strain. Previous strains from 2008 grouped to Wisconsin, Florida, and Brisbane strains. The vaccination campaign that year offered Florida 4/2006 strain in the SH vaccine. Our system did not find influenza B cases in 2007 and 2009. Some samples from 2012 grouped to Wisconsin and Florida as well, but those were not the vaccine selected strains for that year.
The phylogenetic analysis of influenza viruses shows that strains in circulation are similar to the ones detected in the northern part of the hemisphere and the comparison to the northern hemisphere and southern hemisphere vaccine strains shows that only in the case of influenza A/H1N1, the circulating strains coincide with the vaccine strains each year.
One of the limitations of this study is related to RSV circulation in HPTU. A lack of RSV circulation among young children was found, with a very low percentage compared with what has been published in the literature, where RSV was reported as the primary viral agent in children under the age of one. We believe that our results present low numbers of RSV-positive samples because RSV was diagnosed by isolation. We did not perform immunofluorescence from nasopharyngeal secretions directly, but from cultured cells with cytopathic effect. Also, RSV viability is known to be reduced severely when kept out of the −70 C range even for a short period of time, and it is possible that a lapse of time occurred between sample removal and processing, which could have decreased the number of RSV-positive cases. It is also important to mention that the cell lines used in this study work especially well for influenza virus isolation; therefore, although we were able to isolate some RSV, the true number of positive samples may have been missed or gone undiagnosed due to the cell line chosen for isolation. Definitely, RSV circulation in the pediatric population going to HPTU is not as low as this study showed. It would be necessary to develop a specific research to evaluate the real incidence of RSV in HPTU. Another study limitation was the symptomatology reported by the child caregiver, though forwarded by a physician. In addition, sampling was non-probabilistic of consecutive cases of patients seen in both the outpatient area and the emergency room of a high complexity hospital of Medellin; hence, internal validity of these results is meant for the hospital only. The low number of SARI participants does not represent a high impact in the results.
Nevertheless, our passive surveillance study was able to demonstrate the clinical and epidemiologic manifestations of viral respiratory infections in the initial patient visit and the phylogenetic distribution of influenza cases over time, elements that contribute to the relatively sparse description of ILI in a high complexity hospital of Medellin. Future longitudinal studies will help better characterize the clinical course of these patients in Medellin.
This study has allowed us to have a more realistic view of what happens with influenza and other respiratory viruses in the metropolitan area of Medellin. We can assure all studied viruses circulate locally and this contributes to broadening the primary and specialized physicians' observation that we should consider a whole spectrum of respiratory viral agents to implement adequate surveillance measures and a pathology-based treatment.