Clinical characterisation and phylogeny of respiratory syncytial virus infection in hospitalised children at Red Cross War Memorial Children’s Hospital, Cape Town

Respiratory syncytial virus (RSV) is an important cause of bronchiolitis and pneumonia in infants and young children [1]. Globally, it is estimated that RSV causes over 30 million new acute lower respiratory tract infection (LRTI) episodes annually, resulting in more than 3.4 million hospital admissions and199,000 deaths in children younger than 5 years of age [1]. One-third of RSV-related deaths occur in the first year of life, with 96 % of these deaths occurring in low-resource countries [1]. Repeated infections may occur throughout life as immunity following the first RSV infectiondoes not protect against subsequent infections [2]. The infection is spread mainly by close or direct contact with infectious secretions or after touching contaminated surfaces [3]. Risk factors associated with RSV disease include prematurity, cardiopulmonary and immunosuppressive diseases [4]. Nosocomial outbreaks of RSV, which usually coincide with seasonal outbreaks, are a major hazard in paediatric wards, especially in those individuals with increased risk of RSV infection. Nosocomial outbreaks are associated with prolonged hospitalisation and increased mortality compared to community-acquired illness [5‐7]. HIV-infected children also experience prolonged shedding of RSV [6].

RSV is classified into groups A and B based on reactions with monoclonal antibodies against the fusion (F) and attachment (G) glycoproteins [8]. Both groups co-circulate within the community and health care institutions and predominance of one over the other varies by year and geographic location [9, 10]. Many genotypes from each group have been described. New genotypes are continuing to emerge while others are no longer detectable [11, 12]. Although the predominant group and overall patterns of circulating genotypes are distinct for different communities [11],emerging RSV genotypes are also thought to show global spread [13]. Different genotypes may co-circulate within a season, with certain genotypes dominating before being replaced with other genotypes [14, 15]. There are conflicting reports on the association of different groups and genotypes with severity of illness [16‐19]. Ongoing surveillance of the clinical and molecular epidemiology of RSV genotypesis important to characterise prevalent and emerging genotypes that may impact on vaccine development.

The aims of the study were to determine the proportion of RSV nosocomial infections among children testing positive for RSV, describe clinical characteristics of patients with the infection, phylogenetically classify the genotypes causing nosocomial and community-acquired infection, and determine risk factors associated with nosocomial infection in children with acute LRTI, hospitalised at Red Cross War Memorial Children’s Hospital (RCWMCH), Cape Town.

Two-hundred and twenty-six children with PCR-confirmed RSV acute lower respiratory tract infection were identified during the study period, January to October 2012. Figure 1 shows the monthly distribution of community-acquired and nosocomial acute respiratory tract infection associated with RSV. Case detection peaked in May.

In our study of hospitalised children in Cape Town, the RSV cases were recorded from January until October with most cases occurring in May 2012. This is consistent withdata from the severe acute respiratory infections (SARIs) surveillance programme from South Africa which showed that despite circulation throughout the year, the RSV season in the southern hemisphere peaked between February and May [14].

Infants under 6 months of age constituted 71 % of the cohort, which is consistent with a previous study from Kenyain which 58 % of children with RSV were under 6 months of age [25]. In contrast, a study from Indonesia reported the highest incidence of RSV among children aged 6 to 24 months, with low incidence in infants less than 6 months and no cases detected in those under 3 months [26]. These differences may be partially explained by the population-based design, rather than being hospital based [27, 28]. However, another population-based study carried out in the United States found that the highest rate of hospitalisation was in infants who were less than 1 month old [29]. The full explanation for these age differences remain unclear.

In the study cohort, 50 % of the children had pre-existing conditions other than HIV infection. Notable underlying conditions were prematurity (51 %) and congenital heart disease (30 %). Other important conditions were malnutrition and trisomy 21. Unlike the previous study in South Africa carried out when paediatric HIV exposure and infection prevalence was very high in hospitalised children [6, 12], the present study recorded a lower HIV exposure prevalence of 21 % and infection prevalence of only 2 %. The low HIV infection prevalence is primarily due to reduced perinatal HIV transmission resulting from more widely implemented prevention of mother-to-child interventions in South Africa [30]. Prematurity and other high risk conditions however remain prevalent. Immunoprophylaxis may be used in children with underlying conditions as no vaccines currently exist for RSV. Palivizumab has been found to reduce by half the risk of hospitalisation due to RSV infection in these high-risk infants and children, but the high cost prohibits its use in most low- and middle-income countries, including South Africa [31].

Cough was the commonest symptom which was recorded in 86 % of the children, followed by difficulty in breathing (tight chest) in 51 % and fever in 42 %. Wheeze was recorded in only 9 %. Though there was no comparison of the clinical features between RSV positive and RSV negative children in our study, the symptoms were similar to the findings in a study from Pakistan [32]. In that study, the most frequent clinical findings in RSV cases were cough (99 %) and fever (91 %), though wheezing was also present in 91 % of the cases. In the study, clinical features were not statistically significantly different when comparing RSV positive and negative children presenting with acute respiratory infection [32]. In contrast, a study from Jordan that compared presenting symptoms as reported by parents in RSV-positive and RSV-negative children, showed that RSV-positive subjects were more likely to present with cough and shortness of breath and less likely to present with fever, decreased activity, diarrhoea, or vomiting [33]. The differences recorded in the clinical symptoms of RSV may partly explain the limited usefulness of clinical scores. It is desirable to have a clinical index score for RSV disease in order to reduce the use of antibiotics and unnecessary laboratory investigations as well as to facilitate institution of appropriate infection control measures to reduce nosocomial spread. A clinical score which will take into consideration key bronchiolitis symptoms may be useful especially in settings with limited laboratory support and cost. Bronchiolitis symptoms are however not specific to RSV and unfortunately, lack of uniformity of clinical scores and lack of useful association with outcomes have limited their usefulness. Most of the scoring systems have also not been assessed for reliability and validity [34]. Oxygen saturation in a scoring system would also perform poorly in a study cohort of RSV cases such as ours with a high percentage of congenital heart disease and chronic lung disease. It has been suggested that repeat observations may rather provide a more valid overall assessment as the course of bronchiolitis is variable and dynamic [35].

Co-pathogens were detected in 31 % of the patients with RSV infection, most commonly rhinovirus (26 %), adenovirus (14 %) and para-influenza virus (12 %). It is noteworthy that bacterial co-infectionswere only detected in 29 % of our RSV-positive cases while viral co-infections accounted for 62 %. Unsurprisingly, most of these co-pathogens were recovered from the respiratory tract. Although, it may be difficult to determine the relative contributions of the different pathogens that were identified in causing disease or simply colonising the respiratory tract, the presence of any co-pathogen was associated with ventilation, an indicator of severe respiratory tract infection. A high percentage of the patients received antibiotics which was consistent with WHO recommendations to treat all children with pneumonia with antibiotics, to reduce pneumonia-associated mortality [36].

Ten percent of the children in our cohort had nosocomially-acquired RSV infection, similar to findings reported by Madhi et al. [6]. A Canadian multicentre study reported a lower prevalence of 6 % [37]. Nosocomial prevalence rates of more than 20 % have been documented in studies investigating RSV infection in infant, ICU and haematology-oncology units [7, 38, 39]. In the present study, logistic regression analysis showed that the adjusted odds of developing nosocomial infection was more than three-fold greater in children aged6 months or older, compared to younger infants. It is possible that younger children acquire RSV in the community due to the intense transmission and those older represent a specific group of patients in ourhospital. Hall et al reported that the risk of nosocomial infection could not be related to age or underlying disease but rather to the duration of hospital stay [4]. In the study by Madhi et al, nosocomial infection was found to be greater in children with risk factors which included prematurity, congenital heart disease and chronic lung disease [6]. Differences between studies is likely to continue as a result of variations in design, study location and study population. Nosocomial infections should be anticipated when there is a community outbreak and preparations made to prevent in-patients from acquiring the disease during the course of their hospitalisation. Cheng et al. have advocated for regular surveillance of the shedding of virus and confirmation of viral clearance before discontinuation of infection control measures in order to prevent further outbreaks in other patients [40]. Another important consideration which is often overlooked is the role of staff in the spread of RSV infection. About 40 % of medical personnel in an infant ward in one study were shown to have acquired the virus during a nosocomial outbreak and appeared to play a major role as vectors for transmission in the ward. [35] Staff may also continue to be infected from close contact with ill infants or contaminated secretions [41].

RSV A and B groups co-circulated during the 2012 season, although groupA predominated (80 %). Three group A genotypes (NA1, NA2 and ON1) were detected with NA1 predominating (70 %) whereas only one group B genotype (BA4) was detected. The ON1 genotype though first isolated in Canada in 2011 has since been isolated in other settings, including RCWMCH [42]. The ON1 strain was reported to have spread and nearly replaced other RSV A strains in subsequent epidemic seasons in central Italy and Cyprus [13]. The ON1 genotype already appears to have become diversified as variants distinct from the original viruses were found among children admitted to a rural hospital in Kenya during 2012 [43].

A total of 45 ON1 isolates were reported in the present study. A previous study described the first eight ON1 isolates identified at our hospital [42]. The present study showed that the genotype occurred throughout the RSV season and there was no significant difference in its distribution between nosocomial and community-acquired infection. In contrast to Panayiotou et al who reported that the mildest illness was associated with the novel ON1 genotype compared to infections with genotypes GA2 and BA (RSV B) [27], no differences were recorded in the pattern of infection caused by individual RSV groups or genotypes in our study. As the epidemiologic and pathophysiologic characteristics of RSV suggest that there is potential for a different type of vaccine for different target populations [43], the clinical and molecular epidemiology of RSV strains should be monitored to identify new and emerging genotypes.

As with many retrospective studies, some variables could not be analysed as a result of either incompleteness or absence of data. For example, there was no information on breastfeeding or exposure to cigarette smoke in the patient records, and HIV results were not available for some children. The study was limited by being a single centre, single season and the lack of a control group. The convenience sampling method utilised in this study may have inadvertently selected nosocomial cases. Furthermore, the small number of nosocomial cases did not allow for a more rigorous exploration of associations. As the host and viral factors associated with RSV disease are highly dynamic, adequately powered prospective multi-centre studies are required to address these questions, explore the risk factors associated with nosocomial infection in our setting comprehensively, and unravel more facts about this complex virus infection in our setting.

RSV lower respiratory tract infection at RCWMCH has been characterised with a large percentage of children having pre-existing conditions. The majority of children presented with cough and difficulty in breathing. Approximately one tenth of the RSV infections were nosocomial with age 6 months or older a risk factor for nosocomial acquisition. Though both RSV groups co-circulated during the season, group A was predominant, and three different A genotypes were documented including the novel ON1 genotype, first reported in Canada in 2011. Continued surveillance of the clinical epidemiology and phylogeny of RSV strains is important for vaccine development.