Duration of shedding of respiratory syncytial virus in a community study of Kenyan children

Clinical relevance of viral codetection in infants with respiratory syncytial virus bronchiolitis

INTRODUCTION

Respiratory syncytial virus (RSV) is the main cause of severe bronchiolitis, especially in infants. The aim of this study is to assess whether codetection of RSV and other respiratory viruses could affect the severity of this infection comparing with unique RSV detection.

METHODS

A prospective study from 2016 to 2019 including children under 2 years who were admitted in the Emergency Service of the Hospital Universitari Arnau de Vilanova de Lleida (Spain) was performed. Nasopharyngeal samples from all patients were sent to the laboratory for RSV real-time PCR detection (GeneXpert®). A multiplex PCR that detects other respiratory viruses was done in all RSV-positive samples. Patients'medical records were checked to collect clinical data (hospital length of stay, BROSJOD score, ICU admission, need for ventilatory support or transfer to a reference hospital). Patients were divided in two groups: infants with unique RSV detection and infants with viral codetection. Bivariant analyses were performed to analyze the data obtained.

RESULTS

During the period of study 437 RSV bronchiolitis were diagnosed. In 199 of them (177/437; 45,5%) another respiratory virus was detected concomitantly. Bivariant analyses do not show statistically significant differences between both groups.

CONCLUSIONS

Viral codetection in infants with RSV bronchiolitis is frequent. However, it does not seems to affect the severity of this infection.

Modelling respiratory syncytial virus age-specific risk of hospitalisation in term and preterm infants

BACKGROUND

Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory infections in children worldwide. The highest incidence of severe disease is in the first 6 months of life, with infants born preterm at greatest risk for severe RSV infections. The licensure of new RSV therapeutics (a long-acting monoclonal antibody and a maternal vaccine) in Europe, USA, UK and most recently in Australia, has driven the need for strategic decision making on the implementation of RSV immunisation programs. Data driven approaches, considering the local RSV epidemiology, are critical to advise on the optimal use of these therapeutics for effective RSV control.

METHODS

We developed a dynamic compartmental model of RSV transmission fitted to individually-linked population-based laboratory, perinatal and hospitalisation data for 2000-2012 from metropolitan Western Australia (WA), stratified by age and prior exposure. We account for the differential risk of RSV-hospitalisation in full-term and preterm infants (defined as < 37 weeks gestation). We formulated a function relating age, RSV exposure history, and preterm status to the risk of RSV-hospitalisation given infection.

RESULTS

The age-to-risk function shows that risk of hospitalisation, given RSV infection, declines quickly in the first 12 months of life for all infants and is 2.6 times higher in preterm compared with term infants. The hospitalisation risk, given infection, declines to < 10% of the risk at birth by age 7 months for term infants and by 9 months for preterm infants.

CONCLUSIONS

The dynamic model, using the age-to-risk function, characterises RSV epidemiology for metropolitan WA and can now be extended to predict the impact of prevention measures. The stratification of the model by preterm status will enable the comparative assessment of potential strategies in the extended model that target this RSV risk group relative to all-population approaches. Furthermore, the age-to-risk function developed in this work has wider relevance to the epidemiological characterisation of RSV.

Factors Associated With Prolonged Respiratory Virus Detection From Polymerase Chain Reaction of Nasal Specimens Collected Longitudinally in Healthy Children in a US Birth Cohort

BACKGROUND

Respiratory viral shedding is incompletely characterized by existing studies due to the lack of longitudinal nasal sampling and limited inclusion of healthy/asymptomatic children. We describe characteristics associated with prolonged virus detection by polymerase chain reaction (PCR) in a community-based birth cohort.

METHODS

Children were followed from birth to 2 years of age in the PREVAIL cohort. Weekly nasal swabs were collected and tested using the Luminex Respiratory Pathogen Panel. Weekly text surveys were administered to ascertain the presence of acute respiratory illnesses defined as fever and/or cough. Maternal reports and medical chart abstractions identified healthcare utilization. Prolonged virus detection was defined as a persistently positive test lasting ≥4 weeks. Factors associated with prolonged virus detection were assessed using mixed effects multivariable logistic regression.

RESULTS

From a sub-cohort of 101 children with ≥70% weekly swabs collected, a total of 1489 viral infections were detected. Prolonged virus detection was found in 23.4% of viral infections overall, 39% of bocavirus infections, 33% of rhinovirus/enterovirus infections, 14% of respiratory syncytial virus (RSV) A infections, and 7% of RSV B infections. No prolonged detection was found for influenza virus A or B, coronavirus 229E or HKU1, and parainfluenza virus 2 or 4 infections. First-lifetime infection with each virus, and co-detection of another respiratory virus were significantly associated with prolonged detection, while symptom status, child sex, and child age were not.

CONCLUSIONS

Prolonged virus detection was observed in 1 in 4 viral infections in this cohort of healthy children and varied by pathogen, occurring most often for bocavirus and rhinovirus/enterovirus. Evaluating the immunological basis of how viral co-detections and recurrent viral infections impact duration of virus detection by PCR is needed to better understand the dynamics of prolonged viral shedding.

Incidence and transmission of respiratory syncytial virus in urban and rural South Africa, 2017-2018

Data on respiratory syncytial virus (RSV) incidence and household transmission are limited. To describe RSV incidence and transmission, we conducted a prospective cohort study in rural and urban communities in South Africa over two seasons during 2017-2018. Nasopharyngeal swabs were collected twice-weekly for 10 months annually and tested for RSV using PCR. We tested 81,430 samples from 1,116 participants in 225 households (follow-up 90%). 32% (359/1116) of individuals had ≥1 RSV infection; 10% (37/359) had repeat infection during the same season, 33% (132/396) of infections were symptomatic, and 2% (9/396) sought medical care. Incidence was 47.2 infections/100 person-years and highest in children <5 years (78.3). Symptoms were commonest in individuals aged <12 and ≥65 years. Individuals 1-12 years accounted for 55% (134/242) of index cases. Household cumulative infection risk was 11%. On multivariable analysis, index cases with ≥2 symptoms and shedding duration >10 days were more likely to transmit; household contacts aged 1-4 years vs. ≥65 years were more likely to acquire infection. Within two South African communities, RSV attack rate was high, and most infections asymptomatic. Young children were more likely to introduce RSV into the home, and to be infected. Future studies should examine whether vaccines targeting children aged <12 years could reduce community transmission.

Pediatric Respiratory Syncytial Virus Diagnostic Testing Performance: A Systematic Review and Meta-analysis

BACKGROUND

Adding additional specimen types (eg, serology or sputum) to nasopharyngeal swab (NPS) reverse transcription polymerase chain reaction (RT-PCR) increases respiratory syncytial virus (RSV) detection among adults. We assessed if a similar increase occurs in children and quantified underascertainment associated with diagnostic testing.

METHODS

We searched databases for studies involving RSV detection in persons <18 years using ≥2 specimen types or tests. We assessed study quality using a validated checklist. We pooled detection rates by specimen and diagnostic tests and quantified performance.

RESULTS

We included 157 studies. Added testing of additional specimens to NP aspirate (NPA), NPS, and/or nasal swab (NS) RT-PCR resulted in statistically nonsignificant increases in RSV detection. Adding paired serology testing increased RSV detection by 10%, NS by 8%, oropharyngeal swabs by 5%, and NPS by 1%. Compared to RT-PCR, direct fluorescence antibody tests, viral culture, and rapid antigen tests were 87%, 76%, and 74% sensitive, respectively (pooled specificities all ≥98%). Pooled sensitivity of multiplex versus singleplex RT-PCR was 96%.

CONCLUSIONS

RT-PCR was the most sensitive pediatric RSV diagnostic test. Adding multiple specimens did not substantially increase RSV detection, but even small proportional increases could result in meaningful changes in burden estimates. The synergistic effect of adding multiple specimens should be evaluated.

Transient increased risk of influenza infection following RSV infection in South Africa: findings from the PHIRST study, South Africa, 2016-2018

BACKGROUND

Large-scale prevention of respiratory syncytial virus (RSV) infection may have ecological consequences for co-circulating pathogens, including influenza. We assessed if and for how long RSV infection alters the risk for subsequent influenza infection.

METHODS

We analysed a prospective longitudinal cohort study conducted in South Africa between 2016 and 2018. For participating households, nasopharyngeal samples were taken twice weekly, irrespective of symptoms, across three respiratory virus seasons, and real-time polymerase chain reaction (PCR) was used to identify infection with RSV and/or influenza. We fitted an individual-level hidden Markov transmission model in order to estimate RSV and influenza infection rates and their interdependence.

RESULTS

Of a total of 122,113 samples collected, 1265 (1.0%) were positive for influenza and 1002 (0.8%) positive for RSV, with 15 (0.01%) samples from 12 individuals positive for both influenza and RSV. We observed a 2.25-fold higher incidence of co-infection than expected if assuming infections were unrelated. We estimated that infection with influenza is 2.13 (95% CI 0.97-4.69) times more likely when already infected with, and for a week following, RSV infection, adjusted for age. This equates to 1.4% of influenza infections that may be attributable to RSV in this population. Due to the local seasonality (RSV season precedes the influenza season), we were unable to estimate changes in RSV infection risk following influenza infection.

CONCLUSIONS

We find no evidence to suggest that RSV was associated with a subsequent reduced risk of influenza infection. Instead, we observed an increased risk for influenza infection for a short period after infection. However, the impact on population-level transmission dynamics of this individual-level synergistic effect was not measurable in this setting.

Controlled Human Infection Challenge Studies with RSV

Despite considerable momentum in the development of RSV vaccines and therapeutics, there remain substantial barriers to the development and licensing of effective agents, particularly in high-risk populations. The unique immunobiology of RSV and lack of clear protective immunological correlates has held back RSV vaccine development, which, therefore, depends on large and costly clinical trials to demonstrate efficacy. Studies involving the deliberate infection of human volunteers offer an intermediate step between pre-clinical and large-scale studies of natural infection. Human challenge has been used to demonstrate the potential efficacy of vaccines and antivirals while improving our understanding of the protective immunity against RSV infection. Early RSV human infection challenge studies determined the role of routes of administration and size of inoculum on the disease. However, inherent limitations, the use of highly attenuated/laboratory-adapted RSV strains and the continued evolutionary adaptation of RSV limits extrapolation of results to present-day vaccine testing. With advances in technology, it is now possible to perform more detailed investigations of human mucosal immunity against RSV in experimentally infected adults and, more recently, older adults to optimise the design of vaccines and novel therapies. These studies identified defects in RSV-induced humoral and CD8+ T cell immunity that may partly explain susceptibility to recurrent RSV infection. We discuss the insights from human infection challenge models, ethical and logistical considerations, potential benefits, and role in streamlining and accelerating novel antivirals and vaccines against RSV. Finally, we consider how human challenges might be extended to include relevant at-risk populations.

Potential Impact of Nirsevimab on RSV Transmission and Medically Attended Lower Respiratory Tract Illness Caused by RSV: A Disease Transmission Model

INTRODUCTION

Respiratory syncytial virus (RSV) is associated with significant morbidity worldwide, especially among infants. We evaluated the potential impact of prophylactic nirsevimab, a monoclonal antibody, in infants experiencing their first RSV season, and the number of medically-attended lower respiratory tract infection episodes caused by RSV (RSV-MALRTI) in the USA.

METHODS

We developed an age-structured, dynamic, deterministic compartmental model reflecting RSV natural history, incorporating USA demographic data and an age-specific contact matrix. We assumed either no effect of nirsevimab on transmission (scenario 1) or a 50% reduction of viral shedding (scenario 2). Model outcomes were RSV-MALRTIs, ICD-9 coded in the Marketscan^® database by month. We focused on age groups corresponding to the first 2 years of life, during seven RSV seasons (2008-2015).

RESULTS

Scenario 1 illustrated the direct individual benefit when a universal immunization strategy is applied to all infants. In scenario 2, herd protection was observed across age groups, with 15.5% of all avoided cases due to reduced transmission; the greatest impact was in the youngest age group and a benefit was observed in those aged 65+ years.

CONCLUSION

These preliminary data suggest that single-dose nirsevimab will benefit infants experiencing their first RSV season, with a potential increase in effectiveness dependent on nirsevimab's mechanism of action.

Effectiveness and cost-effectiveness of RSV infant and maternal immunization programs: A case study of Nunavik, Canada

BACKGROUND

Despite passive immunization with palivizumab to select high-risk children under two years of age, the health and economic burden of respiratory syncytial virus (RSV) remains substantial. We evaluated the effectiveness and cost-effectiveness of immunization programs with new generations of RSV prophylactics, including long-acting monoclonal antibodies (LAMA) and maternal vaccines, in terms of reducing hospitalizations in Nunavik, a Canadian Arctic region.

METHODS

We developed an agent-based model of RSV transmission and parameterized it with the demographics and burden of RSV in Nunavik, Québec. We compared various immunization strategies, taking into account the costs associated with program delivery and calculating the incremental cost-effectiveness ratio (ICER) using quality-adjusted life-years (QALYs) gained as a measure of effectiveness. Scenario analyses included immunization with palivizumab and LAMA for infants under one year of age, and maternal vaccination in mild, moderate, and severe RSV seasons. Data were analysed from November 1, 2019 to May 1, 2021.

FINDINGS

We found that a Nunavik pilot program with palivizumab which included healthy full-term infants aged 0-2 months in addition to those considered high-risk for complicated RSV disease is not cost-effective, compared to offering palivizumab only to preterm/chronically ill infants under 1 year of age. Using LAMA as prophylaxis produces ICER values of CAD $39,414/QALY (95% Credible Interval [CrI]: $39,314-$40,017) in a mild season (moderately cost-effective) and CAD $5,255/QALY (95% CrI: $5,222-$5,307) in a moderate season (highly cost-effective). LAMA was a dominant (cost-saving with negative incremental costs and positive incremental effects) strategy in a severe RSV season. Maternal vaccination combined with immunization of preterm/chronically ill infants 3-11 months was also a dominant (cost-saving) strategy in all seasons.

INTERPRETATION

The switch from palivizumab in RSV immunization programs to new prophylactics would lead to significant savings, with LAMA being an effective strategy without compromising benefits in terms of reducing hospitalizations.

Evaluating the next generation of RSV intervention strategies: a mathematical modelling study and cost-effectiveness analysis

BACKGROUND

With a suite of promising new RSV prophylactics on the horizon, including long-acting monoclonal antibodies and new vaccines, it is likely that one or more of these will replace the current monoclonal Palivizumab programme. However, choosing the optimal intervention programme will require balancing the costs of the programmes with the health benefits accrued.

METHODS

To compare the next generation of RSV prophylactics, we integrated a novel transmission model with an economic analysis. We estimated key epidemiological parameters by calibrating the model to 7 years of historical epidemiological data using a Bayesian approach. We determined the cost-effective and affordable maximum purchase price for a comprehensive suite of intervention programmes.

FINDINGS

Our transmission model suggests that maternal protection of infants is seasonal, with 38-62% of infants born with protection against RSV. Our economic analysis found that to cost-effectively and affordably replace the current monoclonal antibody Palivizumab programme with long-acting monoclonal antibodies, the purchase price per dose would have to be less than around £4350 but dropping to £200 for vaccinated heightened risk infants or £90 for all infants. A seasonal maternal vaccine would have to be priced less than £85 to be cost-effective and affordable. While vaccinating pre-school and school-age children is likely not cost-effective relative to elderly vaccination programmes, vaccinating the elderly is not likely to be affordable. Conversely, vaccinating infants at 2 months seasonally would be cost-effective and affordable if priced less than £80.

CONCLUSIONS

In a setting with seasonal RSV epidemiology, maternal protection conferred to newborns is also seasonal, an assumption not previously incorporated in transmission models of RSV. For a country with seasonal RSV dynamics like England, seasonal programmes rather than year-round intervention programmes are always optimal.

Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 - A sentinel surveillance report from union territory of Puducherry, India

Background

Acute respiratory infections (ARI) are the most common illnesses affecting people of all ages worldwide. Viruses contribute to 30–70% of acute respiratory infections. Identification of these respiratory viruses is not given high priority except influenza; however, the knowledge about prevalence of non-influenza viruses, their seasonal pattern and genetic evolution have significant epidemiological value.

Methods

As a part of National Influenza-like illness surveillance programme, respiratory specimens were collected children and adults with symptoms of ILI or ARI, between January 2012 and March 2015 (including SARI cases). Real-time PCR was done to identify 13 respiratory viruses. Sequencing was done for representative isolates of each virus using ABI 3730 Genetic Analyzer.

Results

During the study period between January 2012 and March 2015, a total of 648 patients with symptoms of ARI were included in this study. The mean age of the patients was 20.2 years (SD = 19.13, median = 18); 292 (45.1%) were children (≤13 years) and 356 (54.9%) were adults. Respiratory viruses were identified in 44% (287/648) of all patients. Influenza accounted for the maximum number of cases- 179/648 (27.6%). Among the non-influenza viruses, RSV predominated with 34 cases (5.2%), followed by HMPV 24 (3.7%) and PIV-3 20 (3%). Four patients died due to INF A/H1N1 (2012-2, 2015-2) as a result of acute respiratory distress syndrome (ARDS) (CFR 3.7%). Among the non-influenza viruses, no particular seasonality pattern was observed over the different months of the study period.

Conclusion

Antibiotic usage in treating acute respiratory infections empirically is not justified as nearly half of ARI are due to viruses; nearly 28% of them were due to influenza viruses. Among the non-influenza viruses, RSV predominated, followed by HMPV. This study is based on an active influenza surveillance initiated after 2009 pandemic influenza outbreak, in the Union territory of Puducherry which has contributed significantly to the knowledge of the burden of influenza and non-influenza viruses among children and adults. Such surveillance network has paved the way for better diagnosis and timely therapeutic interventions.

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First data on the epidemiology of respiratory viruses from this region after 1974.

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First study to report corona virus, HCoV OC43 from India, and only the second Indian study to document corona virus, HCoV229E. This study is the first study to analyse the genetic sequence of HCoV-229E and OC-43.

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Influenza accounted for the maximum number of cases in the study population, 27%; four patients died of Acute respiratory distress syndrome (ARDS) due to influenza A/H1N1; CFR- 3.7%.

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Among the non-influenza viruses, RSV pre-dominated followed HMPV and PIV-3. No deaths were reported due to non-influenza viral ARI. RSV was detected almost equally in adults and children.

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Distinct pattern was observed in seasonality of influenza viruses but not for non-influenza viruses.

Model evaluation of target product profiles of an infant vaccine against respiratory syncytial virus (RSV) in a developed country setting

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract disease in children worldwide and is a significant cause of hospital admissions in young children in England. No RSV vaccine has been licensed but a number are under development. In this work, we present two structurally distinct mathematical models, parameterized using RSV data from the UK, which have been used to explore the effect of introducing an RSV paediatric vaccine to the National programme. We have explored different vaccine properties, and dosing regimens combined with a range of implementation strategies for RSV control. The results suggest that vaccine properties that confer indirect protection have the greatest effect in reducing the burden of disease in children under 5 years. The findings are reinforced by the concurrence of predictions from the two models with very different epidemiological structure. The approach described has general application in evaluating vaccine target product profiles.

Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice?

Respiratory tract infections (RTIs) are extremely common especially in the first year of life. Knowledge of the etiology of a RTI is essential to facilitate the appropriate management and the implementation of the most effective control measures. This perspective explains why laboratory methods that can identify pathogens in respiratory secretions have been developed over the course of many years. High-complexity multiplex panel assays that can simultaneously detect up to 20 viruses and up to four bacteria within a few hours have been marketed. However, are these platforms actually useful in pediatric clinical practice? In this manuscript, we showed that these platforms appear to be particularly important for epidemiological studies and clinical research. On the contrary, their routine use in pediatric clinical practice remains debatable. They can be used only in the hospital as they require specific equipment and laboratory technicians with considerable knowledge, training, and experience. Moreover, despite more sensitive and specific than other tests routinely used for respiratory pathogen identification, they do not offer significantly advantage for detection of the true etiology of a respiratory disease. Furthermore, knowledge of which virus is the cause of a respiratory disease is not useful from a therapeutic point of view unless influenza virus or respiratory syncytial virus are the infecting agents as effective drugs are available only for these pathogens. On the other hand, multiplex platforms can be justified in the presence of severe clinical manifestations, and in immunocompromised patients for whom specific treatment option can be available, particularly when they can be used simultaneously with platforms that allow identification of antimicrobial resistance to commonly used drugs. It is highly likely that these platforms, particularly those with high sensitivity and specificity and with low turnaround time, will become essential when new drugs effective and safe against most of the respiratory viruses will be available. Further studies on how to differentiate carriers from patients with true disease, as well as studies on the implications of coinfections and identification of antimicrobial resistance, are warranted.

Prolonged shedding of type 55 human adenovirus in immunocompetent adults with adenoviral respiratory infections

Human adenovirus (HAdV) is a common pathogen causing respiratory infections with outbreaks reported in the military and community. However, little information is available on the shedding kinetics. We performed a prospective study of immunocompetent adults confirmed with HAdV respiratory infection by multiplex real-time PCR during an outbreak of HAdV-55. Consecutive respiratory specimens of sputum or nasopharyngeal swab were collected from each patient every 2 days. Viral load was measured by real-time quantitative PCR. Of 32 enrolled patients, 27 (84.4%) had pneumonia. Five patients (15.6%) received cidofovir. Viral load was highest in the earliest samples at 8.69 log₁₀ copies/mL. In a linear regression model, viral load declined consistently in a log-linear fashion at the rate of - 0.15 log₁₀ copies/mL per day (95% confidence interval (CI): - 0.18, - 0.12; R² = 0.32). However, the regression model estimated the viral shedding duration to be 55 days. The rate of decline in viral load did not differ between patients who received cidofovir and who did not. Patients with prominent respiratory symptoms or extensive involvement on chest radiograph had higher volume of viral excretion. Prolonged viral shedding was observed in otherwise healthy adults with HAdV-55 respiratory infection. This finding should be considered in the establishment of infection control and prevention strategies.

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.

Pathogen Clearance and New Respiratory Tract Infections Among Febrile Children in Zanzibar Investigated With Multitargeting Real-Time Polymerase Chain Reaction on Paired Nasopharyngeal Swab Samples

BACKGROUND

New molecular methods have revealed frequent and often polymicrobial respiratory infections in children in low-income settings. It is not known whether presence of multiple pathogens is due to prolonged infections or to frequent exposure. The aim of this study was to analyze short-term pathogen clearance from nasopharynx and the rate of new respiratory tract infections in febrile preschool children.

METHODS

Children (n = 207) with uncomplicated acute febrile illness 2-59 months of age presenting to a health center in Zanzibar, Tanzania, April-July 2011, were included. Paired nasopharyngeal swab samples, collected at enrolment and after 14 days, were analyzed by multiple real-time polymerase chain reaction for Adenovirus, bocavirus, Bordetella pertussis, Chlamydophila pneumoniae, Coronaviruses, Enterovirus, influenza A and B virus, metapneumovirus, measles virus, Mycoplasma pneumoniae, parainfluenza virus, Parechovirus, respiratory syncytial virus and Rhinovirus. An age-matched and geographically matched healthy control group (n = 166) underwent nasopharyngeal sampling on 1 occasion.

RESULTS

At baseline, 157/207 (76%) patients had at least 1 pathogen detected, in total 199 infections. At follow-up (day 14), 162/199 (81%) of these infections were not detected, including >95% of the previously detected infections with Enterovirus, influenza A virus, influenza B virus, metapneumovirus or parainfluenza virus. Still 115 (56%) children were positive for at least 1 pathogen at follow-up, of which 95/115 (83%) were not found at baseline. Detection of influenza B on day 14 was significantly associated with fever during follow-up.

CONCLUSION

The results suggest that children with acute febrile illness in Zanzibar rapidly clear respiratory tract infections but frequently acquire new infections within 14 days.

Simulation of four respiratory viruses and inference of epidemiological parameters

While influenza has been simulated extensively to better understand its behavior and predict future outbreaks, most other respiratory viruses have seldom been simulated. In this study, we provide an overview of four common respiratory viral infections: respiratory syncytial virus (RSV), respiratory adenovirus, rhinovirus and parainfluenza, present specimen data collected 2004–2014, and simulate outbreaks in 19 overlapping regions in the United States. Pairing a compartmental model and data assimilation methods, we infer key epidemiological parameters governing transmission: the basic reproductive number R₀ and length of infection D. RSV had been previously simulated, and our mean estimate of D and R₀ of 5.2 days and 2.8, respectively, are within published clinical and modeling estimates. Among the four virus groupings, mean estimates of R₀ range from 2.3 to 3.0, with a lower and upper quartile range of 2.0–2.8 and 2.6–3.2, respectively. As rapid PCR testing becomes more common, estimates of the observed virulence and duration of infection for these viruses could inform decision making by clinicians and officials for managing patient treatment and response.

The Burden of Human Metapneumovirus and Respiratory Syncytial Virus Infections in Hospitalized Norwegian Children

Background

The burden of severe human metapneumovirus (HMPV) respiratory tract infections (RTIs) in European children has not been clarified. We assessed HMPV in Norwegian children and compared hospitalization rates for HMPV and respiratory syncytial virus (RSV).

Methods

We prospectively enrolled children (<16 years old) hospitalized with RTI and asymptomatic controls (2006-2015). Nasopharyngeal aspirate samples were analyzed with polymerase chain reaction (PCR) tests for HMPV, RSV, and 17 other pathogens. We genotyped HMPV-positive samples and assessed shedding time in 32 HMPV-infected children.

Results

In children with RTI, HMPV was detected in 7.3% (267 of 3650) and RSV in 28.7% (1048 of 3650). Among controls, 2.1% (7 of 339) had low HMPV levels detected by PCR, but all were culture negative. HMPV primarily occurred from January to April and in regular epidemics. At least 2 HMPV subtypes occurred each season. The average annual hospitalization rates in children <5 years old with lower RTI were 1.9/1000 (HMPV) and 10.4/1000 (RSV). Among children with RTI, the median HMPV shedding time by PCR was 13 days (range, 6-28 days), but all were culture negative (noninfectious) after 13 days.

Conclusions

HMPV appears in epidemics in Norwegian children, with a hospitalization rate 5 times lower than RSV. Low levels of HMPV are rarely detected in healthy children.

Quantification and determinants of the amount of respiratory syncytial virus (RSV) shed using real time PCR data from a longitudinal household study

Background: A better understanding of respiratory syncytial virus (RSV) epidemiology requires realistic estimates of RSV shedding patterns, quantities shed, and identification of the related underlying factors. Methods: RSV infection data arise from a cohort study of 47 households with 493 occupants, in coastal Kenya, during the 2009/2010 RSV season. Nasopharyngeal swabs were taken every 3 to 4 days and screened for RSV using a real time polymerase chain reaction (PCR) assay. The amount of virus shed was quantified by calculating the ‘area under the curve’ using the trapezoidal rule applied to rescaled PCR cycle threshold output. Multivariable linear regression was used to identify correlates of amount of virus shed. Results: The median quantity of virus shed per infection episode was 29.4 (95% CI: 15.2, 54.2) log10 ribonucleic acid (RNA) copies. Young age (<1 year), presence of upper respiratory symptoms, intra-household acquisition of infection, an individual’s first infection episode in the RSV season, and having a co-infection of RSV group A and B were associated with increased amount of virus shed. Conclusions: The findings provide insight into which groups of individuals have higher potential for transmission, information which may be useful in designing RSV prevention strategies.

Quantification and determinants of the amount of respiratory syncytial virus (RSV) shed using real time PCR data from a longitudinal household study

Background A better understanding of respiratory syncytial virus (RSV) epidemiology requires realistic estimates of RSV shedding patterns, quantities shed, and identification of the related underlying factors. Methods RSV infection data arise from a cohort study of 47 households with 493 occupants, in coastal Kenya, during the 2009/2010 RSV season. Nasopharyngeal swabs were taken every 3 to 4 days and screened for RSV using a real time polymerase chain reaction (PCR) assay. The amount of virus shed was quantified by calculating the 'area under the curve' using the trapezoidal rule applied to rescaled PCR cycle threshold output. Multivariable linear regression was used to identify correlates of amount of virus shed. Results The median quantity of virus shed per infection episode was 29.4 (95% CI: 15.2, 54.2) log₁₀ ribonucleic acid (RNA) copies. Young age (<1 year), presence of upper respiratory symptoms, intra-household acquisition of infection, an individual's first infection episode in the RSV season, and having a co-infection of RSV group A and B were associated with increased amount of virus shed. Conclusions The findings provide insight into which groups of individuals have higher potential for transmission, information which may be useful in designing RSV prevention strategies.

Vaccination strategies against respiratory syncytial virus

Respiratory syncytial virus (RSV) is the most common cause of US infant hospitalization. Additionally, RSV is responsible for 10,000 deaths annually among the elderly across the United States, and accounts for nearly as many hospitalizations as influenza. Currently, several RSV vaccine candidates are under development to target different age groups. To evaluate the potential effectiveness of age-specific vaccination strategies in averting RSV incidence, we developed a transmission model that integrates data on daily infectious viral load and changes of behavior associated with RSV symptoms. Calibrating to RSV weekly incidence rates in Texas, California, Colorado, and Pennsylvania, we show that in all states considered, an infected child under 5 y of age is more than twice as likely as a person over 50 y of age to transmit the virus. Geographic variability in the effectiveness of a vaccination program across states arises from interplay between seasonality patterns, population demography, vaccination uptake, and vaccine mechanism of action. Regardless of these variabilities, our analysis showed that allocating vaccine to children under 5 y of age would be the most efficient strategy per dose to avert RSV in both children and adults. Furthermore, due to substantial indirect protection, the targeting of children is even predicted to reduce RSV in the elderly more than directly vaccinating the elderly themselves. Our results can help inform ongoing clinical trials and future recommendations on RSV vaccination.

Information content of household-stratified epidemics

Household structure is a key driver of many infectious diseases, as well as a natural target for interventions such as vaccination programs. Many theoretical and conceptual advances on household-stratified epidemic models are relatively recent, but have successfully managed to increase the applicability of such models to practical problems. To be of maximum realism and hence benefit, they require parameterisation from epidemiological data, and while household-stratified final size data has been the traditional source, increasingly time-series infection data from households are becoming available. This paper is concerned with the design of studies aimed at collecting time-series epidemic data in order to maximize the amount of information available to calibrate household models. A design decision involves a trade-off between the number of households to enrol and the sampling frequency. Two commonly used epidemiological study designs are considered: cross-sectional, where different households are sampled at every time point, and cohort, where the same households are followed over the course of the study period. The search for an optimal design uses Bayesian computationally intensive methods to explore the joint parameter-design space combined with the Shannon entropy of the posteriors to estimate the amount of information in each design. For the cross-sectional design, the amount of information increases with the sampling intensity, i.e., the designs with the highest number of time points have the most information. On the other hand, the cohort design often exhibits a trade-off between the number of households sampled and the intensity of follow-up. Our results broadly support the choices made in existing epidemiological data collection studies. Prospective problem-specific use of our computational methods can bring significant benefits in guiding future study designs.

Incorporating Transmission Into Causal Models of Infectious Diseases for Improved Understanding of the Effect and Impact of Risk Factors

Conventional measures of causality (which compare risks between exposed and unexposed individuals) do not factor in the population-scale dynamics of infectious disease transmission. We used mathematical models of 2 childhood infections (respiratory syncytial virus and rotavirus) to illustrate this problem. These models incorporated 3 causal pathways whereby malnutrition could act to increase the incidence of severe infection: increasing the proportion of infected children who develop severe infection, increasing the children's susceptibility to infection, and increasing infectiousness. For risk factors that increased the proportion of infected children who developed severe infection, the population attributable fraction (PAF) calculated conventionally was the same as the PAF calculated directly from the models. However, for risk factors that increased transmission (by either increasing susceptibility to infection or increasing infectiousness), the PAF calculated directly from the models was much larger than that predicted by the conventional PAF calculation. The models also showed that even when conventional studies find no association between a risk factor and an outcome, risk factors that increase transmission can still have a large impact on disease burden. For a complete picture of infectious disease causality, transmission effects must be incorporated into causal models.

Respiratory syncytial virus shedding by children hospitalized with lower respiratory tract infection

Children with respiratory syncytial virus (RSV) infection shed virus for variable periods. The aim of this study was to quantify the viral load in nasopharyngeal aspirates of children with RSV throughout their hospitalization. This study included 37 children who were admitted with a diagnosis of RSV infection based on a positive rapid diagnostic test. Nasopharyngeal aspirates were collected from patients every day, from admission to discharge. Viral detection and quantification were performed using quantitative real-time PCR. Of the 37 patients, RSV-A was detected in 29 and RSV-B in 6. Two patients were PCR-negative for any type of RSV. RSV-A was detected in 12 of 16 patients (75%) 6 days after admission. These patients shed detectable virus from days 1 to 12, and for a significantly longer period (mean 5.7 days) than RSV-B (mean 3.8 days) patients. Half of the RSV-A patients were also positive on day 14 following onset. RSV-A was detected in patients <12 months of age for significantly longer periods after onset than in patients ≥12 months of age. RSV-A viral load was negatively correlated with days from admission and days from onset. Because RSV shedding was frequently prolonged, the hospitalized children may have contracted RSV as a nosocomial infection. To prevent nosocomial RSV infections in hospital wards, healthcare workers must take appropriate infection control measures and provide adequate guidance on hand washing to the family of the patient.

Respiratory Viral Detections During Symptomatic and Asymptomatic Periods in Young Andean Children

BACKGROUND

Viruses are commonly detected in children with acute respiratory illnesses (ARIs) and in asymptomatic children. Longitudinal studies of viral detections during asymptomatic periods surrounding ARI could facilitate interpretation of viral detections but are currently scant.

METHODS

We used reverse transcription polymerase chain reaction to analyze respiratory samples from young Andean children for viruses during asymptomatic periods within 8-120 days of index ARI (cough or fever). We compared viral detections over time within children and explored reverse transcription polymerase chain reaction cycle thresholds (CTs) as surrogates for viral loads.

RESULTS

At least 1 respiratory virus was detected in 367 (43%) of 859 samples collected during asymptomatic periods, with more frequent detections in periods with rhinorrhea (49%) than those without (34%, P < 0.001). Relative to index ARI with human rhinovirus (HRV), adenovirus (AdV), respiratory syncytial virus (RSV) and parainfluenza virus detected, the same viruses were also detected during 32, 22, 10 and 3% of asymptomatic periods, respectively. RSV was only detected 8-30 days after index RSV ARI, whereas HRV and AdV were detected throughout asymptomatic periods. Human metapneumovirus and influenza were rarely detected during asymptomatic periods (<3%). No significant differences were observed in the CT for HRV or AdV during asymptomatic periods relative to ARI. For RSV, CTs were significantly lower during ARI relative to the asymptomatic period (P = 0.03).

CONCLUSIONS

These findings indicate that influenza, human metapneumovirus, parainfluenza virus and RSV detections in children with an ARI usually indicate a causal relationship. When HRV or AdV is detected during ARI, the causal relationship is less certain.

Vaccine Induced Herd Immunity for Control of Respiratory Syncytial Virus Disease in a Low-Income Country Setting

Background

Respiratory syncytial virus (RSV) is globally ubiquitous, and infection during the first six months of life is a major risk for severe disease and hospital admission; consequently RSV is the most important viral cause of respiratory morbidity and mortality in young children. Development of vaccines for young infants is complicated by the presence of maternal antibodies and immunological immaturity, but vaccines targeted at older children avoid these problems. Vaccine development for young infants has been unsuccessful, but this is not the case for older children (> 6m). Would vaccinating older children have a significant public health impact? We developed a mathematical model to explore the benefits of a vaccine against RSV.

Methods and Findings

We have used a deterministic age structured model capturing the key epidemiological characteristics of RSV and performed a statistical maximum-likelihood fit to age-specific hospitalization data from a developing country setting. To explore the effects of vaccination under different mixing assumptions, we included two versions of contact matrices: one from a social contact diary study, and the second a synthesised construction based on demographic data. Vaccination is assumed to elicit an immune response equivalent to primary infection. Our results show that immunisation of young children (5–10m) is likely to be a highly effective method of protection of infants (<6m) against hospitalisation. The majority benefit is derived from indirect protection (herd immunity). A full sensitivity and uncertainty analysis using Latin Hypercube Sampling of the parameter space shows that our results are robust to model structure and model parameters.

Conclusions

This result suggests that vaccinating older infants and children against RSV can have a major public health benefit.

Evaluating vaccination strategies for reducing infant respiratory syncytial virus infection in low-income settings

BACKGROUND

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract disease and related hospitalization of young children in least developed countries. Individuals are repeatedly infected, but it is the first exposure, often in early infancy, that results in the vast majority of severe RSV disease. Unfortunately, due to immunological immaturity, infants are a problematic RSV vaccine target. Several trials are ongoing to identify a suitable candidate vaccine and target group, but no immunization program is yet in place.

METHODS

In this work, an individual-based model that explicitly accounts for the socio-demographic population structure is developed to investigate RSV transmission patterns in a rural setting of Kenya and to evaluate the potential effectiveness of alternative population targets in reducing RSV infant infection.

RESULTS

We find that household transmission is responsible for 39% of infant infections and that school-age children are the main source of infection within the household, causing around 55% of cases. Moreover, assuming a vaccine-induced protection equivalent to that of natural infection, our results show that annual vaccination of students is the only alternative strategy to routine immunization of infants able to trigger a relevant and persistent reduction of infant infection (on average, of 35.6% versus 41.5% in 10 years of vaccination). Interestingly, if vaccination of pregnant women boosts maternal antibody protection in infants by an additional 4 months, RSV infant infection will be reduced by 31.5%.

CONCLUSIONS

These preliminary evaluations support the efforts to develop vaccines and related strategies that go beyond targeting vaccines to those at highest risk of severe disease.

Environmental drivers of the spatiotemporal dynamics of respiratory syncytial virus in the United States

Epidemics of respiratory syncytial virus (RSV) are known to occur in wintertime in temperate countries including the United States, but there is a limited understanding of the importance of climatic drivers in determining the seasonality of RSV. In the United States, RSV activity is highly spatially structured, with seasonal peaks beginning in Florida in November through December and ending in the upper Midwest in February-March, and prolonged disease activity in the southeastern US. Using data on both age-specific hospitalizations and laboratory reports of RSV in the US, and employing a combination of statistical and mechanistic epidemic modeling, we examined the association between environmental variables and state-specific measures of RSV seasonality. Temperature, vapor pressure, precipitation, and potential evapotranspiration (PET) were significantly associated with the timing of RSV activity across states in univariate exploratory analyses. The amplitude and timing of seasonality in the transmission rate was significantly correlated with seasonal fluctuations in PET, and negatively correlated with mean vapor pressure, minimum temperature, and precipitation. States with low mean vapor pressure and the largest seasonal variation in PET tended to experience biennial patterns of RSV activity, with alternating years of “early-big” and “late-small” epidemics. Our model for the transmission dynamics of RSV was able to replicate these biennial transitions at higher amplitudes of seasonality in the transmission rate. This successfully connects environmental drivers to the epidemic dynamics of RSV; however, it does not fully explain why RSV activity begins in Florida, one of the warmest states, when RSV is a winter-seasonal pathogen. Understanding and predicting the seasonality of RSV is essential in determining the optimal timing of immunoprophylaxis.

Respiratory syncytial virus (RSV) causes annual outbreaks of respiratory disease every winter in temperate climates, which can be severe particularly among infants. In the United States, RSV activity begins each autumn in Florida and appears to spread from the southeast to the northwest. Using data on hospitalizations and laboratory tests for RSV, we show that the timing of epidemics is associated with a variety of climatic factors, including temperature, vapor pressure, precipitation, and potential evapotranspiration (PET). Furthermore, using a dynamic model, we show that seasonal variation in the transmission rate of RSV can be correlated with the amplitude and timing of variation in PET, which is a measure of demand for water from the atmosphere. States with colder, drier weather and a large seasonal swing in PET tended to experience an alternating pattern of “early-big” RSV epidemics one year followed by a “late-small” epidemic the next year, which our model was able to reproduce based on the interaction between susceptible and infectious individuals. However, we cannot fully explain why epidemics begin in Florida. Being able to understand and predict the timing of RSV activity is important for optimizing the delivery of immunoprophylaxis to high-risk individuals.

Transmission of respiratory syncytial virus infection within families

Half of all family members of children hospitalized with RSV infection were positive for RSV around the time of the child's admission. In most cases, the likely source of the infant's RSV infection was an older sibling or a parent.

Background. Because the production of an effective respiratory syncytial virus (RSV) vaccine for infants is challenging, vaccination of other family members is one viable alternative to prevent severe RSV illnesses in infants.

Methods. In a prospective study, we enrolled all family members of children who were hospitalized with RSV infection. Nasal swabs for RSV detection were obtained from all participating family members. Data on respiratory symptoms in the family members prior to and after the child's admission were collected using standardized questionnaires.

Results. At the time of or within 1 week after the index child's hospitalization, RSV was detected in 40 (77%) of the 52 families and in 60 (47%) of 129 family members. Forty-nine (82%) of RSV detections in the family members were associated with respiratory symptoms. A sibling or a parent was the probable primary case of RSV in 30 (58%) families. Respiratory syncytial virus loads in the nasal swabs were significantly higher (10^7.7) in index children than in their parents (10^5.1, P < .0001).

Conclusions. In most cases, the likely source of an infant's RSV infection is an older sibling or a parent. These findings support the strategy of reducing the burden of RSV in infants by vaccination of their family members.

Measles-mumps-rubella vaccination and respiratory syncytial virus-associated hospital contact

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MMR vaccination is given to protect against measles, mumps and rubella.

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RSV is an important cause of acute lower respiratory infections in young children.

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MMR vaccination was associated with 22% lower rate of RSV hospital contacts.

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MMR vaccination may reduce the rate or severity of RSV infection.

Background

The live measles vaccine has been associated with lower non-measles mortality and admissions in low-income countries. The live measles–mumps–rubella vaccine has also been associated with lower rate of admissions with any type of infection in Danish children; the association was strongest for admissions with lower respiratory infections.

Objective

To examine whether measles, mumps, and rubella (MMR) vaccination was associated with reduced rate of hospital contact related to respiratory syncytial virus (RSV) in a high-income country.

Methods

Nationwide cohort study of laboratory-confirmed RSV hospital contacts at age 14–23 months in all children born in Denmark 1997–2002 who had already received the vaccine against diphtheria, tetanus, pertussis (acellular), polio, and Haemophilus influenzae type b (DTaP-IPV-Hib) at the recommended ages of 3, 5, and 12 months.

Results

The study included 888 RSV hospital contacts in 128,588 person years of follow up (rate 6.8/1000 person years). Having MMR as the most recent vaccine was associated with a reduced rate of RSV hospital contacts compared with having DTaP-IPV-Hib as the most recent vaccine (Incidence rate ratio (IRR), 0.75; 95% confidence interval (CI), 0.63–0.89). After adjustment for potential confounders including exact age in days the IRR was 0.78 (95% CI, 0.66–0.93). The adjusted IRR was 0.74 (95% CI, 0.60–0.92) in males and 0.84 (95% CI, 0.66–1.06) in females (P Interaction, 0.42). There was no association in the first month after MMR vaccination (adjusted IRR, 0.97; 95% CI, 0.76–1.24) but the adjusted IRR was 0.70 (95% CI, 0.58–0.85) from one month after MMR vaccination.

Conclusions

MMR vaccination was associated with reduced rate of hospital contacts related to laboratory-confirmed RSV infection. Further research on the association between MMR vaccination and other unrelated pathogens are warranted.

Immunity to RSV in Early-Life

Respiratory Syncytial Virus (RSV) is the commonest cause of severe respiratory infection in infants, leading to over 3 million hospitalizations and around 66,000 deaths worldwide each year. RSV bronchiolitis predominantly strikes apparently healthy infants, with age as the principal risk factor for severe disease. The differences in the immune response to RSV in the very young are likely to be key to determining the clinical outcome of this common infection. Remarkable age-related differences in innate cytokine responses follow recognition of RSV by numerous pattern recognition receptors, and the importance of this early response is supported by polymorphisms in many early innate genes, which associate with bronchiolitis. In the absence of strong, Th1 polarizing signals, infants develop T cell responses that can be biased away from protective Th1 and cytotoxic T cell immunity toward dysregulated, Th2 and Th17 polarization. This may contribute not only to the initial inflammation in bronchiolitis, but also to the long-term increased risk of developing wheeze and asthma later in life. An early-life vaccine for RSV will need to overcome the difficulties of generating a protective response in infants, and the proven risks associated with generating an inappropriate response. Infantile T follicular helper and B cell responses are immature, but maternal antibodies can afford some protection. Thus, maternal vaccination is a promising alternative approach. However, even in adults adaptive immunity following natural infection is poorly protective, allowing re-infection even with the same strain of RSV. This gives us few clues as to how effective vaccination could be achieved. Challenges remain in understanding how respiratory immunity matures with age, and the external factors influencing its development. Determining why some infants develop bronchiolitis should lead to new therapies to lessen the clinical impact of RSV and aid the rational design of protective vaccines.

Modelling the seasonal epidemics of respiratory syncytial virus in young children

BACKGROUND

Respiratory syncytial virus (RSV) is a major cause of paediatric morbidity. Mathematical models can be used to characterise annual RSV seasonal epidemics and are a valuable tool to assess the impact of future vaccines.

OBJECTIVES

Construct a mathematical model of seasonal epidemics of RSV and by fitting to a population-level RSV dataset, obtain a better understanding of RSV transmission dynamics.

METHODS

We obtained an extensive dataset of weekly RSV testing data in children aged less than 2 years, 2000-2005, for a birth cohort of 245,249 children through linkage of laboratory and birth record datasets. We constructed a seasonally forced compartmental age-structured Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) mathematical model to fit to the seasonal curves of positive RSV detections using the Nelder-Mead method.

RESULTS

From 15,830 specimens, 3,394 were positive for RSV. RSV detections exhibited a distinct biennial seasonal pattern with alternating sized peaks in winter months. Our SEIRS model accurately mimicked the observed data with alternating sized peaks using disease parameter values that remained constant across the 6 years of data. Variations in the duration of immunity and recovery periods were explored. The best fit to the data minimising the residual sum of errors was a model using estimates based on previous models in the literature for the infectious period and a slightly lower estimate for the immunity period.

CONCLUSIONS

Our age-structured model based on routinely collected population laboratory data accurately captures the observed seasonal epidemic curves. The compartmental SEIRS model, based on several assumptions, now provides a validated base model. Ranges for the disease parameters in the model that could replicate the patterns in the data were identified. Areas for future model developments include fitting climatic variables to the seasonal parameter, allowing parameters to vary according to age and implementing a newborn vaccination program to predict the effect on RSV incidence.

Influence of age, severity of infection, and co-infection on the duration of respiratory syncytial virus (RSV) shedding

RSV is the most important viral cause of pneumonia and bronchiolitis in children worldwide and has been associated with significant disease burden. With the renewed interest in RSV vaccines, we provide realistic estimates on duration, and influencing factors on RSV shedding which are required to better understand the impact of vaccination on the virus transmission dynamics. The data arise from a prospective study of 47 households (493 individuals) in rural Kenya, followed through a 6-month period of an RSV seasonal outbreak. Deep nasopharyngeal swabs were collected twice each week from all household members, irrespective of symptoms, and tested for RSV by multiplex PCR. The RSV G gene was sequenced. A total of 205 RSV infection episodes were detected in 179 individuals from 40 different households. The infection data were interval censored and assuming a random event time between observations, the average duration of virus shedding was 11·2 (95% confidence interval 10·1-12·3) days. The shedding durations were longer than previous estimates (3·9-7·4 days) based on immunofluorescence antigen detection or viral culture, and were shown to be strongly associated with age, severity of infection, and revealed potential interaction with other respiratory viruses. These findings are key to our understanding of the spread of this important virus and are relevant in the design of control programmes.

Kinetics of the neutralizing antibody response to respiratory syncytial virus infections in a birth cohort

The kinetics of respiratory syncytial virus (RSV) neutralizing antibodies following birth, primary and secondary infections are poorly defined. The aims of the study were to measure and compare neutralizing antibody responses at different time points in a birth cohort followed-up over three RSV epidemics. Rural Kenyan children, recruited at birth between 2002 and 2003, were monitored for RSV infection over three epidemic seasons. Cord and 3-monthly sera, and acute and convalescent sera following RSV infection, were assayed in 28 children by plaque reduction neutralization test (PRNT). Relative to the neutralizing antibody titers of pre-exposure control sera (1.8 log10 PRNT), antibody titers following primary infection were (i) no different in sera collected between 0 and 0.4 months post-infection (1.9 log10 PRNT, P=0.146), (ii) higher in sera collected between 0.5 and 0.9 (2.8 log10 PRNT, P<0.0001), 1.0-1.9 (2.5 log10 PRNT, P<0.0001), and 2.0-2.9 (2.3 log10 PRNT, P<0.001) months post-infection, and (iii) no different in sera collected at between 3.0 and 3.9 months post-infection (2.0 log10 PRNT, P=0.052). The early serum neutralizing response to secondary infection (3.02 log10 PRNT) was significantly greater than the early primary response (1.9 log10 PRNT, P<0.0001). Variation in population-level virus transmission corresponded with changes in the mean cohort-level neutralizing titers. It is concluded that following primary RSV infection the neutralizing antibody response declines to pre-infection levels rapidly (~3 months) which may facilitate repeat infection. The kinetics of the aggregate levels of acquired antibody reflect seasonal RSV occurrence, age, and infection history.

Using mathematical transmission modelling to investigate drivers of respiratory syncytial virus seasonality in children in the Philippines

We used a mathematical transmission model to estimate when ecological drivers of respiratory syncytial virus (RSV) transmissibility would need to act in order to produce the observed seasonality of RSV in the Philippines. We estimated that a seasonal peak in transmissibility would need to occur approximately 51 days prior to the observed peak in RSV cases (range 49 to 67 days). We then compared this estimated seasonal pattern of transmissibility to the seasonal patterns of possible ecological drivers of transmissibility: rainfall, humidity and temperature patterns, nutritional status, and school holidays. The timing of the seasonal patterns of nutritional status and rainfall were both consistent with the estimated seasonal pattern of transmissibility and these are both plausible drivers of the seasonality of RSV in this setting.

Dynamics of infectious diseases

Modern infectious disease epidemiology has a strong history of using mathematics both for prediction and to gain a deeper understanding. However the study of infectious diseases is a highly interdisciplinary subject requiring insights from multiple disciplines, in particular a biological knowledge of the pathogen, a statistical description of the available data and a mathematical framework for prediction. Here we begin with the basic building blocks of infectious disease epidemiology--the SIS and SIR type models--before considering the progress that has been made over the recent decades and the challenges that lie ahead. Throughout we focus on the understanding that can be developed from relatively simple models, although accurate prediction will inevitably require far greater complexity beyond the scope of this review. In particular, we focus on three critical aspects of infectious disease models that we feel fundamentally shape their dynamics: heterogeneously structured populations, stochasticity and spatial structure. Throughout we relate the mathematical models and their results to a variety of real-world problems.

Molecular epidemiology of respiratory syncytial virus transmission in childcare

Background

Respiratory syncytial virus (RSV) is the most important cause of serious respiratory infections in young children. No prior studies using molecular techniques to examine RSV transmission in the community childcare setting have been performed.

Objectives

We seek to characterize the molecular epidemiology of RSV transmission in childcare to evaluate the impact of RSV disease in a community-based population.

Methods

We sequenced RSV-positive nasopharyngeal samples from a prospective longitudinal study of respiratory illnesses among children enrolled in childcare during three winter seasons. Phylogenetic analysis was performed to identify unique viral strains.

Results

RSV was detected in 59 (11%) illnesses. Compared to RSV-negative illnesses, RSV-positive illnesses were associated with longer symptom duration and increased frequency of health care visits. Another respiratory virus was detected in 42 (71%) RSV-positive illnesses. RSV viral load did not differ between RSV-positive illnesses with and without another respiratory virus identified (P = 0.38). In two childcare rooms, 50% of the children had RSV detected within six days of the first case. Five (38%) of 13 illness episodes from one childcare room were sequenced and shown to be the same viral strain, suggesting rapid child-to-child transmission within the room over a 16 day period.

Conclusions

RSV is rapidly transmitted within childcare. Childcare facilities may serve as ideal sites for evaluation of new prevention strategies given the high burden of RSV disease in this population and the rapidity of RSV spread between children.

Does respiratory virus coinfection increases the clinical severity of acute respiratory infection among children infected with respiratory syncytial virus?

BACKGROUND

Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory infection in children less than 5 years of age. The impact of non-RSV respiratory virus coinfection on the severity of RSV disease is unknown.

METHODS

This hospital-based prospective study was conducted in Nagasaki, Japan, on all children less than 5 years of age with acute respiratory infection (ARI) who had undergone a rapid RSV diagnostic test between April 2009 and March 2010. Thirteen respiratory viruses were identified from nasopharyngeal swab samples using a multiplex polymerase chain reaction; polymerase chain reaction-positive samples were considered as confirmed respiratory virus infections. The cases were classified into 3 categories (pneumonia, moderate-to-severe nonpneumonic ARI and mild ARI) according to the findings of the chest radiograph and the hospitalization records.

RESULTS

Among 384 cases enrolled, 371 were eligible for analysis, of whom 85 (23%) were classified as pneumonia cases; 137 (37%) as moderate-to-severe nonpneumonic ARI cases and 162 (40%) as mild ARI cases. RSV was detected in 172 cases (61.6%), and 31 cases (18.0%) had double or triple infections with other respiratory viruses. RSV infection was more frequently observed in pneumonia cases (odds ratio [OR]: 2.3; 95% confidence interval [CI]: 1.31-3.9) and moderate-to-severe nonpneumonic ARI cases (OR: 2.95; 95% CI: 1.82-4.78) than in mild ARI cases. The association with moderate-to-severe nonpneumonic ARI cases was stronger with RSV/non-RSV respiratory virus coinfection (adjusted OR: 4.91; 95% CI: 1.9-12.7) than with RSV single infection (adjusted OR: 2.77; 95% CI: 1.64-4.7).

CONCLUSIONS

Non-RSV respiratory virus coinfection is not uncommon in RSV-infected children and may increase the severity of RSV disease.

The incidence and clinical burden of respiratory syncytial virus disease identified through hospital outpatient presentations in Kenyan children

Background

There is little information that describe the burden of respiratory syncytial virus (RSV) associated disease in the tropical African outpatient setting.

Methods

We studied a systematic sample of children aged <5 years presenting to a rural district hospital in Kenya with acute respiratory infection (ARI) between May 2002 and April 2004. We collected clinical data and screened nasal wash samples for RSV antigen by immunofluorescence. We used a linked demographic surveillance system to estimate disease incidence.

Results

Among 2143 children tested, 166 (8%) were RSV positive (6% among children with upper respiratory tract infection and 12% among children with lower respiratory tract infection (LRTI). RSV was more likely in LRTI than URTI (p<0.001). 51% of RSV cases were aged 1 year or over. RSV cases represented 3.4% of hospital outpatient presentations. Relative to RSV negative cases, RSV positive cases were more likely to have crackles (RR = 1.63; 95% CI 1.34–1.97), nasal flaring (RR = 2.66; 95% CI 1.40–5.04), in-drawing (RR = 2.24; 95% CI 1.47–3.40), fast breathing for age (RR = 1.34; 95% CI 1.03–1.75) and fever (RR = 1.54; 95% CI 1.33–1.80). The estimated incidence of RSV-ARI and RSV-LRTI, per 100,000 child years, among those aged <5 years was 767 and 283, respectively.

Conclusion

The burden of childhood RSV-associated URTI and LRTI presenting to outpatients in this setting is considerable. The clinical features of cases associated with an RSV infection were more severe than cases without an RSV diagnosis.

Genetic relatedness of infecting and reinfecting respiratory syncytial virus strains identified in a birth cohort from rural Kenya

Background. Respiratory syncytial virus (RSV) reinfects individuals repeatedly. The extent to which this is a consequence of RSV antigenic diversity is unclear.

Methods. Six-hundred thirty-five children from rural Kenya were closely monitored for RSV infection from birth through 3 consecutive RSV epidemics. RSV infections were identified by immunofluorescence testing of nasal washing samples collected during acute respiratory illnesses, typed into group A and B, and sequenced in the attachment (G) protein. A positive sample separated from a previous positive by ≥14 days was defined as a reinfection a priori.

Results. Phylogenetic analysis was undertaken for 325 (80%) of 409 identified infections, including 53 (64%) of 83 reinfections. Heterologous group reinfections were observed in 28 episodes, and homologous group reinfections were observed in 25 episodes; 10 involved homologous genotypes, 5 showed no amino acid changes, and 3 were separated by 21–24 days and were potentially persistent infections. The temporal distribution of genotypes among reinfections did not differ from that of single infections.

Conclusions. The vast majority of infection and reinfection pairs differed by group, genotype, or G amino acid sequence (ie, comprised distinct viruses). The extent to which this is a consequence of immune memory of infection history or prevalent diversity remains unclear.

A frequentist approach to estimating the force of infection for a respiratory disease using repeated measurement data from a birth cohort

This article aims to develop a probability-based model involving the use of direct likelihood formulation and generalised linear modelling (GLM) approaches useful in estimating important disease parameters from longitudinal or repeated measurement data. The current application is based on infection with respiratory syncytial virus. The force of infection and the recovery rate or per capita loss of infection are the parameters of interest. However, because of the limitation arising from the study design and subsequently, the data generated only the force of infection is estimable. The problem of dealing with time-varying disease parameters is also addressed in the article by fitting piecewise constant parameters over time via the GLM approach. The current model formulation is based on that published in White LJ, Buttery J, Cooper B, Nokes DJ and Medley GF. Rotavirus within day care centres in Oxfordshire, UK: characterization of partial immunity. Journal of Royal Society Interface 2008; 5: 1481–1490 with an application to rotavirus transmission and immunity.

Optimal design of studies of influenza transmission in households. I: case-ascertained studies

Case-ascertained household transmission studies, in which households including an 'index case' are recruited and followed up, are invaluable to understanding the epidemiology of influenza. We used a simulation approach parameterized with data from household transmission studies to evaluate alternative study designs. We compared studies that relied on self-reported illness in household contacts vs. studies that used home visits to collect swab specimens for virological confirmation of secondary infections, allowing for the trade-off between sample size vs. intensity of follow-up given a fixed budget. For studies estimating the secondary attack proportion, 2-3 follow-up visits with specimens collected from all members regardless of illness were optimal. However, for studies comparing secondary attack proportions between two or more groups, such as controlled intervention studies, designs with reactive home visits following illness reports in contacts were most powerful, while a design with one home visit optimally timed also performed well.