Molecular epidemiological analysis of a nosocomial outbreak of respiratory syncytial virus associated pneumonia in a kangaroo mother care unit in South Africa

An outbreak of RSV infections in a neonatology clinic during the RSV-season

BACKGROUND

Respiratory syncytial virus (RSV) is the predominant cause of lower respiratory tract infections (LRTI) in infancy. Preterm infants with bronchopulmonary dysplasia (BPD) are at the highest risk of severe RSV-LRTI. This is a retrospective study that analyses a nosocomial outbreak of RSV infections in the Neonatology clinic of the University Hospital of Obstetrics and Gynecology, Sofia, 2019.

METHODS

Two groups of infants without contact between them were diagnosed with RSV-infection: 14 infants were treated in the Department for healthy newborns - Group 1, and 7 preterm infants were treated in the Neonatal Intensive Care Unit (NICU) - Group 2. The detection of RSV was performed using Real-Time PCR in nasal/throat swabs.

RESULTS

Respiratory symptoms occurred 2-5 days after discharge in 14 of 148 healthy term infants born February 5 to 18, 2019; 12 babies were re-hospitalized with LRTI and recovered in a few days. RSV-PCR was positive in 6 infants, while in the others, RSV etiology was suggested, due to similar symptoms and contact between them. The first NICU patient with RSV-LRTI was one of the 26 gestational weeks (GW) twins, who had severe BPD. The other twin was always discharged home without LRTI-symptoms. In the period February 19 to March 15, 2019, 26 premature babies born at 26-34 GW, were tested for RSV (33 nasal/throat swabs). They received a first or subsequent palivizumab injection. We identified 11 positive samples in 7 of the babies. Despite the clinical recovery, the second RSV-PCR remained positive in 4 babies. Six of the 7 NICU patients had symptoms of LRTI, and two of them needed mechanical ventilation. Six babies were discharged home after stabilization, one was transferred to the Pediatric department for further treatment of BPD and later discharged too.

CONCLUSIONS

This was the most serious outbreak of RSV infections in neonates since the RSV-PCR diagnostic in Bulgaria was introduced. The course of RSV-LRTI was severe in extremely preterm patients with underlying BPD. So, routine in-hospital RSV-prophylaxis with palivizumab should be considered for infants at the highest risk.

Multiple Respiratory Syncytial Virus Introductions Into a Neonatal Intensive Care Unit

BACKGROUND

Outbreaks of respiratory syncytial virus (RSV) in neonatal intensive care units (NICUs) are of concern because of the risk of severe disease in young infants. We describe an outbreak of RSV in a NICU and use whole genome sequencing (WGS) to better understand the relatedness of viruses among patients.

METHODS

An investigation was conducted to identify patients and describe their clinical course. Infection control measures were implemented to prevent further spread. Respiratory specimens from outbreak-related patients and the community were tested using WGS. Phylogenetic trees were constructed to understand relatedness of the viruses.

RESULTS

Seven patients developed respiratory symptoms within an 11-day span in December 2017 and were diagnosed with RSV; 6 patients (86%) were preterm and 1 had chronic lung disease. Three patients required additional respiratory support after symptom onset, and none died. Six of 7 patients were part of the same cluster based on > 99.99% nucleotide agreement with each other and 3 unique single-nucleotide polymorphisms were identified in viruses sequenced from those patients. The seventh patient was admitted from the community with respiratory symptoms and had a genetically distinct virus that was not related to the other 6. Implementation of enhanced infection control measures likely limited the spread.

CONCLUSIONS

Using WGS, we found 2 distinct introductions of RSV into a NICU, highlighting the risk of healthcare-associated infections during RSV season. Early recognition and infection control measures likely limited spread, emphasizing the importance of considering RSV in the differential diagnosis of respiratory infections in healthcare settings.

Viral Respiratory Infections in the Neonatal Intensive Care Unit-A Review

Although infrequent, respiratory viral infections (RVIs) during birth hospitalization have a significant impact on short- and long-term morbidity in term and preterm neonates. RVI have been associated with increased length of hospital stay, severe disease course, unnecessary antimicrobial exposure and nosocomial outbreaks in the neonatal intensive care unit (NICU). Virus transmission has been described to occur via health care professionals, parents and other visitors. Most at risk are infants born prematurely, due to their immature immune system and the fact that they stay in the NICU for a considerable length of time. A prevalence of RVIs in the NICU in symptomatic infants of 6–30% has been described, although RVIs are most probably underdiagnosed, since testing for viral pathogens is not performed routinely in symptomatic patients in many NICUs. Additional challenges are the wide range of clinical presentation of RVIs, their similarity to bacterial infections and the unreliable detection methods prior to the era of molecular biology based technologies. In this review, current knowledge of early-life RVI in the NICU is discussed. Reviewed viral pathogens include human rhinovirus, respiratory syncytial virus and influenza virus, and discussed literature is restricted to reports based on modern molecular biology techniques. The review highlights therapeutic approaches and possible preventive strategies. Furthermore, short- and long-term consequences of RVIs in infants hospitalized in the NICU are discussed.

BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics

Respiratory syncytial virus (RSV) is an important pathogen of global significance. The BA9 is one of the most predominant lineages of the BA genotype of group B RSV that has acquired a 60bp duplication in its G protein gene. We describe the local and global evolutionary dynamics of the second hyper variable region in the C- terminal of the G protein gene of the BA9 lineage. A total of 418 sequences (including 31 study and 387 GenBank strains) from 29 different countries were used for phylogenetic analysis. This analysis showed that the study strains clustered with BA (BA9 and BA8) and SAB4 genotype of group B RSV. We performed time-scaled evolutionary clock analyses using Bayesian Markov chain Monte Carlo methods. We also carried out glycosylation, selection pressure, mutational, entropy and Network analyses of the BA9 lineage. The time to the most recent common ancestor (tMRCA) of the BA genotype and BA9 lineage were estimated to be the years 1995 (95% HPD; 1987–1997) and 2000 (95% HPD; 1998–2001), respectively. The nucleotide substitution rate of the BA genotype [(4.58×10⁻³ (95% HPD; 3.89–5.29×10⁻³) substitution/site/year] was slightly faster than the BA9 lineage [4.03×10⁻³ (95% HPD; 4.65–5.2492×10⁻³)]. The BA9 lineage was categorized into 3 sub lineages (I, II and III) based on the Bayesian and Network analyses. The local transmission pattern suggested that BA9 is the predominant lineage of BA viruses that has been circulating in India since 2002 though showing fluctuations in its effective population size. The BA9 lineage established its global distribution with report from 23 different countries over the past 16 years. The present study augments our understanding of RSV infection, its epidemiological dynamics warranting steps towards its overall global surveillance.

Infectious disease exposures and outbreaks at a South African neonatal unit with review of neonatal outbreak epidemiology in Africa

BACKGROUND

Hospitalized neonates are vulnerable to infection, with pathogen exposures occurring in utero, intrapartum, and postnatally. African neonatal units are at high risk of outbreaks owing to overcrowding, understaffing, and shared equipment.

METHODS

Neonatal outbreaks attended by the paediatric infectious diseases and infection prevention (IP) teams at Tygerberg Children's Hospital, Cape Town (May 1, 2008 to April 30, 2016) are described, pathogens, outbreak size, mortality, source, and outbreak control measures. Neonatal outbreaks reported from Africa (January 1, 1996 to January 1, 2016) were reviewed to contextualize the authors' experience within the published literature from the region.

RESULTS

Thirteen outbreaks affecting 148 babies (11 deaths; 7% mortality) over an 8-year period were documented, with pathogens including rotavirus, influenza virus, measles virus, and multidrug-resistant bacteria (Serratia marcescens, Acinetobacter baumannii, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant enterococci). Although the infection source was seldom identified, most outbreaks were associated with breaches in IP practices. Stringent transmission-based precautions, staff/parent education, and changes to clinical practices contained the outbreaks. From the African neonatal literature, 20 outbreaks affecting 524 babies (177 deaths; 34% mortality) were identified; 50% of outbreaks were caused by extended-spectrum β-lactamase-producing Klebsiella pneumoniae.

CONCLUSIONS

Outbreaks in hospitalized African neonates are frequent but under-reported, with high mortality and a predominance of Gram-negative bacteria. Breaches in IP practice are commonly implicated, with the outbreak source confirmed in less than 50% of cases. Programmes to improve IP practice and address antimicrobial resistance in African neonatal units are urgently required.

Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014

Respiratory syncytial virus (RSV) is an important viral pathogen of acute respiratory tract infection (ARI). Limited data are available on molecular epidemiology of RSV from Saudi Arabia. A total of 130 nasopharyngeal aspirates were collected from children less than 5 years of age with ARI symptoms attending the Emergency Department at King Khalid University Hospital and King Fahad Medical City, Riyadh, Saudi Arabia between October and December, 2014. RSV was identified in the 26% of the hospitalized children by reverse transcriptase PCR. Group A RSV (77%) predominated during the study as compared to group B RSV (23%). The phylogenetic analysis of 28 study strains clustered group A RSV in NA1 and ON1 genotypes and group B viruses in BA (BA9) genotype. Interestingly, 26% of the positive samples clustered in genotypes with duplication in the G protein gene (ON1 for group A and BA for group B). Both the genotypes showed enhanced O-linked glycosylation in the duplicated region, with 10 and 2 additional sites in ON1 and BA respectively. Selection pressure analysis revealed purifying selection in both the ON1 and BA genotypes. One codon each in the ON1 (position 274) and BA genotypes (position 219) were positively selected and had high entropy values indicating variations at these amino acid positions. This is the first report describing the presence of ON1 genotype and the first report on co-circulation of two different genotypes of RSV with duplication in the G protein gene from Saudi Arabia. The clinical implications of the simultaneous occurrence of genotypes with duplication in G protein gene in a given population especially in the concurrent infections should be investigated in future. Further, the ongoing surveillance of RSV in this region will reveal the evolutionary trajectory of these two genotypes with duplication in G protein gene from largest country in the Middle East.

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

BACKGROUND

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children in both the community and hospital setting.

METHODS

The clinical presentation, patient and phylogenetic characteristicsof laboratory-confirmed cases of RSV, as well as risk factors for nosocomial infectionat Red Cross War Memorial Children's Hospital in Cape Town were analysed. A multiplex PCR assay that detects 7 respiratory viruses was used to identify RSV nucleic acid on respiratory specimens.

RESULTS

A total of 226 children were studied, ages ranging between 1 week and 92.5 months (median: 2.8 months, IQR: 1.3-6.3 months) and 51.8 % were males. The median duration of symptoms prior to diagnosis was 2 days (IQR: 1-4 days). Nosocomial infections wereidentified in 22 (9.7 %) children. There were pre-existing medical conditions in 113 (50.0 %) excluding HIV, most commonly prematurity (n = 58, 50.0 %) and congenital heart disease (n = 34, 29.3 %). The commonest presenting symptoms were cough (196, 86.7 %), difficulty in breathing (115, 50.9 %) and fever (91, 41.6 %).A case fatality rate of 0.9 % was recorded. RSV group A predominated (n = 181, 80.1 %) while group B accounted for only 45 (19.9 %) of the infections. The prevalent genotypes were NA1 (n = 127,70.1 %), ON1 (n = 45,24.9 %) and NA2 (n = 9,5.0 %) for group A while the only circulating RSV B genotype was BA4. There was no significant difference in the genotype distribution between the nosocomial and community-acquired RSV infections. Age ≥ 6 months was independently associated with nosocomial infection.

CONCLUSIONS

A large percentage of children with RSV infection had pre-existing conditions. Approximately one tenth of the infections were nosocomial with age 6 months or older being a risk factor. Though both RSV groups co-circulated during the season, group A was predominant and included the novel ON1 genotype. Continued surveillance is necessary to identify prevalent and newly emerging genotypes ahead of vaccine development and efficacy studies.

Risk of nosocomial respiratory syncytial virus infection and effectiveness of control measures to prevent transmission events: a systematic review

Respiratory syncytial virus (RSV) causes a significant public health burden, and outbreaks among vulnerable patients in hospital settings are of particular concern. We reviewed published and unpublished literature from hospital settings to assess: (i) nosocomial RSV transmission risk (attack rate) during outbreaks, (ii) effectiveness of infection control measures. We searched the following databases: MEDLINE, EMBASE, CINAHL, Cochrane Library, together with key websites, journals and grey literature, to end of 2012. Risk of bias was assessed using the Cochrane risk of bias tool or Newcastle–Ottawa scale. A narrative synthesis was conducted. Forty studies were included (19 addressing research question one, 21 addressing question two). RSV transmission risk varied by hospital setting; 6–56% (median: 28·5%) in neonatal/paediatric settings (n = 14), 6–12% (median: 7%) in adult haematology and transplant units (n = 3), and 30–32% in other adult settings (n = 2). For question two, most studies (n = 13) employed multi‐component interventions (e.g. cohort nursing, personal protective equipment (PPE), isolation), and these were largely reported to be effective in reducing nosocomial transmission. Four studies examined staff PPE; eye protection appeared more effective than gowns and masks. One study reported on RSV prophylaxis for patients (RSV‐Ig/palivizumab); there was no statistical evidence of effectiveness although the sample size was small. Overall, risk of bias for included studies tended to be high. We conclude that RSV transmission risk varies widely during hospital outbreaks. Although multi‐component control strategies appear broadly successful, further research is required to disaggregate the effectiveness of individual components including the potential role of palivizumab prophylaxis.

Preventing Cleavage of the Respiratory Syncytial Virus Attachment Protein in Vero Cells Rescues the Infectivity of Progeny Virus for Primary Human Airway Cultures

All live attenuated respiratory syncytial virus (RSV) vaccines that have advanced to clinical trials have been produced in Vero cells. The attachment (G) glycoprotein in virions produced in these cells is smaller than that produced in other immortalized cells due to cleavage. These virions are 5-fold less infectious for primary well-differentiated human airway epithelial (HAE) cell cultures. Because HAE cells are isolated directly from human airways, Vero cell-grown vaccine virus would very likely be similarly inefficient at initiating infection of the nasal epithelium following vaccination, and therefore, a larger inoculum would be required for effective vaccination. We hypothesized that Vero cell-derived virus containing an intact G protein would be more infectious for HAE cell cultures. Using protease inhibitors with increasing specificity, we identified cathepsin L to be the protease responsible for cleavage. Our evidence suggests that cleavage occurs in the late endosome or lysosome during endocytic recycling. Cathepsin L activity was 100-fold greater in Vero cells than in HeLa cells. In addition, cathepsin L was able to cleave the G protein in Vero cell-grown virions but not in HeLa cell-grown virions, suggesting a difference in G-protein posttranslational modification in the two cell lines. We identified by mutagenesis amino acids important for cleavage, and these amino acids included a likely cathepsin L cleavage site. Virus containing a modified, noncleavable G protein produced in Vero cells was 5-fold more infectious for HAE cells in culture, confirming our hypothesis and indicating the value of including such a mutation in future live attenuated RSV vaccines.

IMPORTANCE

Worldwide, RSV is the second leading infectious cause of infant death, but no vaccine is available. Experimental live attenuated RSV vaccines are grown in Vero cells, but during production the virion attachment (G) glycoprotein is cleaved. Virions containing a cleaved G protein are less infectious for primary airway epithelial cells, the natural RSV target. In the study described here we identified the protease responsible, located the cleavage site, and demonstrated that cleavage likely occurs during endocytic recycling. Moreover, we showed that the infectivity of Vero cell-derived virus for primary airway epithelial cells is increased 5-fold if the virus contains a mutation in the G protein that prevents cleavage. The blocking of cleavage should improve RSV vaccine yield, consequently reducing production costs. Posttranslational cleavage of the fusion glycoprotein of many viruses plays an essential role in activation; however, cleavage of the RSV G protein is a novel example of a detrimental effect of cleavage on virus infectivity.

Skin-to-Skin Care for Term and Preterm Infants in the Neonatal ICU

“Kangaroo mother care” was first described as an alternative method of caring for low birth weight infants in resource-limited countries, where neonatal mortality and infection rates are high because of overcrowded nurseries, inadequate staffing, and lack of equipment. Intermittent skin-to-skin care (SSC), a modified version of kangaroo mother care, is now being offered in resource-rich countries to infants needing neonatal intensive care, including those who require ventilator support or are extremely premature. SSC significantly improves milk production by the mother and is associated with a longer duration of breastfeeding. Increased parent satisfaction, better sleep organization, a longer duration of quiet sleep, and decreased pain perception during procedures have also been reported in association with SSC. Despite apparent physiologic stability during SSC, it is prudent that infants in the NICU have continuous cardiovascular monitoring and that care be taken to verify correct head positioning for airway patency as well as the stability of the endotracheal tube, arterial and venous access devices, and other life support equipment.

Molecular characterization of human respiratory syncytial virus subtype B: a novel genotype of subtype B circulating in China

Human respiratory syncytial virus (HRSV) is major pathogen of lower respiratory tract infections in infants and young children worldwide. There have been many studies regarding HRSV subgroup A (HRSV-A) G protein genetic variability but little information about HRSV subtype B (HRSV-B) G protein genetic diversity and molecular evolution in China. Thus, a survey of the molecular epidemiology and evolution of the G protein in China is of high importance. In this study, the circulation and genetic diversity of HRSV in Chongqing, Southwestern China, from June 2009 to May 2013, were investigated. A total of 3,167 nasopharyngeal aspirates were obtained in this study, and it was found that HRSV-B predominated in the 2009-2010 and 2012-2013 epidemic seasons. This study identified the genetic variability of the glycoprotein G gene among 102 HRSV-B strains isolated by cell culture from Chongqing nasopharyngeal aspirates, and 68 Chinese HRSV-B sequences were deposited in GenBank. Genotyping and phylogenetic analysis revealed that the HRSV-B strains were clustered into three genotypes: BA (n = 111, 65.29%), GB3 (n = 5, 2.94%), and a new GB genotype (n = 54, 31.77%) named GB5. The GB5 strains varied from other genotypes in the central conserved region and N-glycosylation sites. The estimated evolutionary rate of Chinese HRSV-B was 2.01 × 10(-3) nucleotide substitutions/site/year, which is similar to the reports from Belgium and the Netherlands with 1.95 × 10(-3) and 2.78 × 10(-3) nucleotide substitutions/site/year, respectively. This study provides data on the circulating pattern and molecular characterization of HRSV-B genotypes in China during four consecutive years and may contribute to HRSV vaccine development.

Evaluation of respiratory syncytial virus group A and B genotypes among nosocomial and community-acquired pediatric infections in Southern Brazil

BACKGROUND

Respiratory syncytial virus (RSV) is the main cause of lower respiratory tract illness in children worldwide. Molecular analyses show two distinct RSV groups (A and B) that comprise different genotypes. This variability contributes to the capacity of RSV to cause yearly outbreaks. These RSV genotypes circulate within the community and within hospital wards. RSV is currently the leading cause of nosocomial respiratory tract infections in pediatric populations. The aim of this study was to evaluate the G protein gene diversity of RSV amplicons.

METHODS

Nasopharyngeal aspirate samples were collected from children with nosocomial or community-acquired infections. Sixty-three RSV samples (21 nosocomial and 42 community-acquired) were evaluated and classified as RSV-A or RSV-B by real-time PCR. Sequencing of the second variable region of the G protein gene was performed to establish RSV phylogenetics.

RESULTS

We observed co-circulation of RSV-A and RSV-B, with RSV-A as the predominant group. All nosocomial and community-acquired RSV-A samples were from the same phylogenetic group, comprising the NA1 genotype, and all RSV-B samples (nosocomial and community-acquired) were of the BA4 genotype. Therefore, in both RSV groups (nosocomial and community-acquired), the isolates belonged to only one genotype in circulation.

CONCLUSIONS

This is the first study to describe circulation of the NA1 RSV genotype in Brazil. Furthermore, this study showed that the BA4 genotype remains in circulation. Deciphering worldwide RSV genetic variability will aid vaccine design and development.

Replacement and positive evolution of subtype A and B respiratory syncytial virus G-protein genotypes from 1997-2012 in South Africa

BACKGROUND

Of the respiratory syncytial virus (RSV) genotypes previously described in South Africa during 1997-2002, only GA2 and GA5 persisted until 2006, with BA having replaced all previous RSV-B genotypes. This poses the question whether RSV-A is more stable than RSV-B and whether positive selection drives evolution of genotypes.

METHODS

RSV-positive specimens were randomly selected during 2009-2012, subtyped, sequenced, and compared to RSV recovered from specimens obtained during 1997-2001 and 2006-2009. Bayesian phylogenetic analysis was performed on the G-protein.

RESULTS

Phylogenetic analysis indicated that RSV-A genotype GA2 dissolved to form SAA2 (unique to South Africa), NA1 and NA2 (identified in Japan), and ON1 (identified in Canada and having a 72-bp insertion) and that GA5 drifted from 1999-2012 to form 3 subgenotypes (GA5 I-III). RSV-B genotypes all had the 60-bp insertion typical of BA genotypes but clustered into subgenotypes BA8-10. Positive selection was identified in the G-protein of both subtypes, but RSV-A's rate of evolution was slower than that of RSV-B, with the most recent common ancestors dating from 1945 and 1951, respectively. Seven new positively selected sites were identified in South African strains, 2 for RSV-A and 5 for RSV-B.

CONCLUSION

Positive selection drove both RSV-A and -B genotypes to evolve, resulting in replacement of all genotypes over the 15-year study period in South Africa.

Detection of respiratory viral infections in neonates treated for suspicion of nosocomial bacterial sepsis: a feasibility study

There is a lack of knowledge concerning the frequency and significance of respiratory viral infections that occur in the neonatal intensive care unit. In the present study, all neonates with suspected nosocomial bacterial sepsis were screened for a panel of respiratory viruses. Respiratory viral infections were detected in 10% of these cases. This was comparable with the frequency of a blood-culture-proven sepsis.

Molecular characterization of a respiratory syncytial virus outbreak in a hematology unit in Heidelberg, Germany

In 2011 and 2012, a large outbreak of respiratory syncytial virus (RSV) infections affecting 57 laboratory-confirmed patients occurred in an adult hematology unit in Heidelberg, Germany. During the outbreak investigation, we performed molecular genotyping of RSV strains to differentiate between single versus multiple introductions of the virus into the unit. Furthermore, we assessed the time of viral shedding of consecutive samples from the patients in order to better understand the possible impact of prolonged shedding for outbreak control management. We used subtype-specific reverse transcription-PCR on nasopharyngeal and bronchoalveolar specimens for routine diagnostics and for measuring the viral shedding period. Samples of 47 RSV-infected patients involved in the outbreak were genotyped by sequence analysis and compared to samples from RSV-infected hospitalized children representing the timing of the annual RSV epidemic in the community. Molecular investigation of the virus strains from clinical samples revealed a unique cluster with identical nucleotide sequences of RSV type A (RSV A outbreak strain) for 41 patients, while 3 patients were infected with different RSV A (nonoutbreak) strains and three other patients with RSV type B. Outbreak strains were identified in samples from November 2011 until January 2012, while nonoutbreak strains were from samples coinciding with the community epidemic in February and March 2012. Median duration of viral shedding time was 24.5 days (range, 1 to 168 days) with no difference between outbreak and nonoutbreak strains (P = 0.45). Our investigation suggests a single introduction of the RSV A outbreak strain into the unit that spread among the immunocompromised patients. Prolonged viral shedding may have contributed to nosocomial transmission and should be taken into account in the infection control management of RSV outbreaks in settings with heavily immunosuppressed patients.

Diagnosis of respiratory syncytial virus infection

Respiratory syncytial virus (RSV) is one of the most important pathogen causing severe lower respiratory tract infections in all age groups often requiring hospitalization. Rapid laboratory diagnosis of RSV infection significantly decreases the use of antibiotics, additional laboratory testing and is associated with shorter hospitalization periods. The specific diagnosis of RSV infection is based on the detection of virus or viral antigens or virus specific nucleic acid sequences in respiratory secretions. The kind and quality of the clinical specimen exerts a considerable influence on the results of all currently used viral detection assays. Antigen based tests are widely available, easy to perform and the results are available in a short time but their reduced sensitivity and specificity represent a considerable shortcoming. Among the methods available isolation in cell culture was considered the gold standard for the sensitive identification of RSV but is gradually replaced by highly sensitive and specific nucleic acid amplification assays that provide more rapid results. Of these reverse transcription polymerase chain reaction (PCR) was the first and is still the most frequently used nucleic acid-based assay. New methodologies, as for example the real-time PCR methods allow the quantification of viral nucleic acids in the clinical sample. Disadvantages of the nucleic acid based assays are their high costs and their limited standardization.

Future research on new methodologies for the diagnosis of viral respiratory tract infections should focus on the development of sensitive, rapid and cost effective test systems allowing the screening for all probable causative agents. In addition varying testing protocols for summer and winter months based on epidemiologic data are needed to direct their practical use.

Molecular epidemiology of the SH (small hydrophobic) gene of human respiratory syncytial virus (HRSV), over 2 consecutive years

Human respiratory syncytial virus (HRSV) strains were isolated from nasopharyngeal aspirates collected from 965 children between 2004 and 2005, yielding 424 positive samples. We sequenced the small hydrophobic protein (SH) gene of 117 strains and compared them with other viruses identified worldwide. Phylogenetic analysis showed a low genetic variability among the isolates but allowed us to classify the viruses into different genotypes for both groups, HRSVA and HRSVB. It is also shown that the novel BA-like genotype was well segregated from the others, indicating that the mutations are not limited to the G gene.

Circulating strains of human respiratory syncytial virus in central and south America

Human respiratory syncytial virus (HRSV) is a major cause of viral lower respiratory tract infections among infants and young children. HRSV strains vary genetically and antigenically and have been classified into two broad subgroups, A and B (HRSV-A and HRSV-B, respectively). To date, little is known about the circulating strains of HRSV in Latin America. We have evaluated the genetic diversity of 96 HRSV strains by sequencing a variable region of the G protein gene of isolates collected from 2007 to 2009 in Central and South America. Our results show the presence of the two antigenic subgroups of HRSV during this period with the majority belonging to the genotype HRSV-A2.

Replacement of previously circulating respiratory syncytial virus subtype B strains with the BA genotype in South Africa

Respiratory syncytial virus (RSV) is a major cause of bronchiolitis and pneumonia in infants, the immunocompromised, and the elderly in both developed and developing countries. Reinfections are common, and G protein variability is one mechanism to overcome herd immunity. This is illustrated by the appearance of the BA genotype with a 60-nucleotide duplication dominating the subtype B genotypes in epidemics worldwide. To investigate the evolution of subtype B in South Africa since 2002, the genetic variability of the G protein was analyzed in all recent strains isolated over 4 years (2006 to 2009) in South African hospitals. Bayesian analysis revealed a replacement of all subtype B genotypes previously identified in South Africa with the BA genotype since 2006, while subtype A genotypes identified in previous years are still circulating. Compared to BA strains from other countries, the evolutionary rate of the South African BA genotype was shown to be 2.305 × 10(-3) nucleotide substitutions/site/year and drift was evident. The most recent common ancestor (MRCA) of the South African BA viruses was determined to date back to 1996. All South African BA isolates clustered with the BA-IV subgenotype, and the appearance of new subgenotypes within this branch may occur if drift continues. Sequencing of the complete G protein of selected South African strains revealed an additional 6-nucleotide deletion. Acquisition of the 60-nucleotide duplication appeared to have improved the fitness of this virus, and more recent subtype B strains may need to be included in experimental vaccines to evaluate their efficacy in the current setting of evolved circulating strains.

Identification of deletion mutant respiratory syncytial virus strains lacking most of the G protein in immunocompromised children with pneumonia in South Africa

Respiratory syncytial virus (RSV) G protein deletion mutants replicate effectively in vitro but have not been detected in nature. Subtyping of RSV strains in hospitalized children in South Africa identified G protein PCR amplicons significantly reduced in size in 2 out of 209 clinical specimens screened over 4 years. Sequence analysis revealed subtype B strains lacking nearly the entire G protein ectodomain in one HIV-positive and one HIV-exposed child hospitalized with pneumonia. The association of clinical strains lacking most of the G protein with lower respiratory tract infection in immunocompromised children may have implications for RSV vaccine development.

Molecular diagnosis of viral respiratory infections

In clinical practice, a rapid and accurate identification of pathogens causing viral respiratory tract infections can be problematic because of nonspecific clinical presentations, lack of rapid and sensitive tests, and the emergence of new and mutating viral pathogens. Nucleic acid-targeted molecular techniques are increasingly being used to provide high sensitivity and specificity, short test turnaround time, and automatic and high-throughput processing. In-house and commercially available molecular methods have been developed to qualitatively and quantitatively detect and identify a single or a panel of clinically encountered respiratory tract viruses in a single reaction. Molecular techniques are being gradually introduced in routine laboratory diagnosis of viral respiratory tract infections. However, their performance characteristics and limitations must be clearly understood by both laboratory personnel and clinicians to ensure proper utilization and interpretation.

Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nucleotide duplication in the G protein gene

The emergence of natural isolates of human respiratory syncytial virus group B (HRSV-B) with a 60-nucleotide (nt) duplication in the G protein gene in Buenos Aires, Argentina, in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003) and their dissemination worldwide allowed us to use the duplicated segment as a natural tag to examine in detail the evolution of HRSV during propagation in its natural host. Viruses with the duplicated segment were all clustered in a new genotype, named BA (A. Trento et al., J. Virol. 80:975-984, 2006). To obtain information about the prevalence of these viruses in Spain, we tested for the presence of the duplicated segment in positive HRSV-B clinical samples collected at the Severo Ochoa Hospital (Madrid) during 12 consecutive epidemics (1996-1997 to 2007-2008). Viruses with the 60-nt duplication were found in 61 samples, with a high prevalence relative to the rest of B genotypes in the most recent seasons. Global phylogenetic and demographic analysis of all G sequences containing the duplication, collected across five continents up until April 2009, revealed that the prevalence of the BA genotype increased gradually until 2004-2005, despite its rapid dissemination worldwide. After that date and coinciding with a bottleneck effect on the population size, a relatively new BA lineage (BA-IV) replaced all other group B viruses, suggesting further adaptation of the BA genotype to its natural host.

Nosocomial RSV infection control and outbreak management

The incidence of nosocomial respiratory syncytial virus (RSV) infection in different areas of the world is not well known. However, it is clear that RSV infection of hospitalized infants with congenital heart disease or following preterm birth is highly relevant. Nosocomial RSV infection in these high-risk group infants often follows a severe course of disease, even resulting in mortality. Transmission of RSV mainly occurs through direct contact, but not through inhalation. Consequently, prevention of nosocomial RSV infection should aim to prevent direct contact between non-infected infants and RSV-infected people. Evidence of the role of gowns, masks and gloves is discussed. The effect and safety of cohorting RSV-infected infants is reviewed. International guidelines with respect to RSV prevention and outbreak management are analysed.