Genomic Analysis and Surveillance of Respiratory Syncytial Virus (RSV) Using Wastewater-Based Epidemiology (WBE).

Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack of predictable seasonal dynamics limits the public health response. Wastewater-based epidemiology (WBE) has recently been used globally as a key metric in determining prevalence of SARS-CoV-2 in the community but its application to other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, applying RT-qPCR and partial G-gene sequencing to track RSV levels and variants in the community. We report increasing detection of RSV in wastewater concomitant with increasing numbers of positive clinical cases. Analysis of wastewater-derived RSV sequences permitted identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance and aid the management of RSV by informing the timely deployment of pharmaceutical and non-pharmaceutical interventions.

A Text Mining Approach to Explore IFNε Literature and Biological Mechanisms.

Interferons (IFN) constitute a primary line of protection against mucosal infection, with IFN research spanning over 60 years and encompassing a vast ever-expanding amount of literature. Most of what is currently understood has been derived from extensive research defining the roles of "classical" type I IFNs, IFNα and IFNß. However, little is known regarding responses elicited by less well-characterized IFN subtypes such as IFNε. In this paper, we combined a deductive text mining analysis of IFNε literature characterizing literature-derived knowledge with a comparative analysis of other type I and type III IFNs. Utilizing these approaches, three clusters of terms were extracted from the literature covering different aspects of IFNε research and a set of 47 genes uniquely cited in the context of IFNε. The use of these "in silico" approaches support the expansion of current understanding and the creation of new knowledge surrounding IFNε.

Review of the Safety, Efficacy and Tolerability of Palivizumab in the Prevention of Severe Respiratory Syncytial Virus (RSV) Disease.

Respiratory Syncytial Virus (RSV) is a major global cause of childhood morbidity and mortality. Palivizumab, a monoclonal antibody that provides passive immunity against RSV, is currently licensed for prophylactic use in specific "high-risk" populations, including congenital heart disease, bronchopulmonary dysplasia and prematurity. Available research suggests palivizumab use in these high-risk populations can lead to a reduction in RSV-related hospitalization. However, palivizumab has not been demonstrated to reduce mortality, adverse events or length of hospital stay related to RSV. In this article, we review the management of RSV, indications for palivizumab prophylaxis, the safety, cost-effectiveness and efficacy of this preventative medication, and emerging therapeutics that could revolutionize future prevention of this significant pathogen.

The effect of the COVID-19 pandemic on influenza-related hospitalization, intensive care admission and mortality in children in Canada: A population-based study.

Background: The COVID-19 pandemic resulted in unprecedented implementation of wide-ranging public health measures globally. During the pandemic, dramatic decreases in seasonal influenza virus detection have been reported worldwide. Information on the impact on paediatric influenza-related hospitalisations is limited. We describe influenza-related hospitalisation in children in Canada following the onset of the COVID-19 pandemic. Methods: Data on influenza-related hospitalisations, intensive care unit (ICU) admissions and in-hospital deaths in children across Canada were obtained from the Canadian Immunisation Monitoring Program, ACTive (IMPACT). This national active surveillance initiative comprises 90% of all tertiary care paediatric beds in Canada. The study period included eleven influenza seasons, from the 2010/2011 season until the 2020/2021 season inclusive. Time series modelling was used to compare the observed to predicted influenza-related hospitalisations following the COVID-19 pandemic. Results: Following the COVID-19 pandemic there was a significant decrease in paediatric influenza-related hospitalisations compared to predicted influenza-related hospitalisations for this time period (p < 0•0001). No paediatric influenza-related hospitalisations, ICU admission or deaths were reported for the 2020/2021 influenza season. Conclusions: We show complete absence of paediatric influenza infection-related hospitalisation in a Canadian National Surveillance Network during the 2020/2021 influenza season. This significant decrease is likely related in large part to non-pharmacological public health interventions implemented during the COVID-19 pandemic, although the potential role of viral interference is unknown. Funding: The Canadian Immunisation Monitoring Program, Active (IMPACT) influenza surveillance is a national surveillance initiative managed by the Canadian Paediatric Society and conducted by the IMPACT network of paediatric investigators on behalf of the Public Health Agency of Canada's Centre for Immunisation and Respiratory Infectious Diseases.

The impact of the COVID-19 pandemic on influenza, respiratory syncytial virus, and other seasonal respiratory virus circulation in Canada: A population-based study.

BACKGROUND: The ongoing coronavirus disease 2019 (COVID-19) pandemic has resulted in implementation of public health measures worldwide to mitigate disease spread, including; travel restrictions, lockdowns, messaging on handwashing, use of face coverings and physical distancing. As the pandemic progresses, exceptional decreases in seasonal respiratory viruses are increasingly reported. We aimed to evaluate the impact of the pandemic on laboratory confirmed detection of seasonal non-SARS-CoV-2 respiratory viruses in Canada. METHODS: Epidemiologic data were obtained from the Canadian Respiratory Virus Detection Surveillance System. Weekly data from the week ending 30th August 2014 until the week ending the 13th March 2021 were analysed. We compared trends in laboratory detection and test volumes during the 2020/2021 season with pre-pandemic seasons from 2014 to 2019. FINDINGS: We observed a dramatically lower percentage of tests positive for all seasonal respiratory viruses during 2020-2021 compared to pre-pandemic seasons. For influenza A and B the percent positive decreased to 0•0015 and 0•0028 times that of pre-pandemic levels respectively and for RSV, the percent positive dropped to 0•0169 times that of pre-pandemic levels. Ongoing detection of enterovirus/rhinovirus occurred, with regional variation in the epidemic patterns and intensity. INTERPRETATION: We report an effective absence of the annual seasonal epidemic of most seasonal respiratory viruses in 2020/2021. This dramatic decrease is likely related to implementation of multi-layered public health measures during the pandemic. The impact of such measures may have relevance for public health practice in mitigating seasonal respiratory virus epidemics and for informing responses to future respiratory virus pandemics. FUNDING: No additional funding source was required for this study.

The differential impact of pediatric COVID-19 between high-income countries and low- and middle-income countries: A systematic review of fatality and ICU admission in children worldwide.

BACKGROUND: The overall global impact of COVID-19 in children and regional variability in pediatric outcomes are presently unknown. METHODS: To evaluate the magnitude of global COVID-19 death and intensive care unit (ICU) admission in children aged 0-19 years, a systematic review was conducted for articles and national reports as of December 7, 2020. This systematic review is registered with PROSPERO (registration number: CRD42020179696). RESULTS: We reviewed 16,027 articles as well as 225 national reports from 216 countries. Among the 3,788 global pediatric COVID-19 deaths, 3,394 (91.5%) deaths were reported from low- and middle-income countries (LMIC), while 83.5% of pediatric population from all included countries were from LMIC. The pediatric deaths/1,000,000 children and case fatality rate (CFR) were significantly higher in LMIC than in high-income countries (HIC) (2.77 in LMIC vs 1.32 in HIC; p < 0.001 and 0.24% in LMIC vs 0.01% in HIC; p < 0.001, respectively). The ICU admission/1,000,000 children was 18.80 and 1.48 in HIC and LMIC, respectively (p < 0.001). The highest deaths/1,000,000 children and CFR were in infants < 1 year old (10.03 and 0.58% in the world, 5.39 and 0.07% in HIC and 10.98 and 1.30% in LMIC, respectively). CONCLUSIONS: The study highlights that there may be a larger impact of pediatric COVID-19 fatality in LMICs compared to HICs.

Initial Guidance on Use of Monoclonal Antibody Therapy for Treatment of Coronavirus Disease 2019 in Children and Adolescents.

BACKGROUND: In November 2020, the US Food and Drug Administration (FDA) provided Emergency Use Authorizations (EUA) for 2 novel virus-neutralizing monoclonal antibody therapies, bamlanivimab and REGN-COV2 (casirivimab plus imdevimab), for the treatment of mild to moderate coronavirus disease 2019 (COVID-19) in adolescents and adults in specified high-risk groups. This has challenged clinicians to determine the best approach to use of these products. METHODS: A panel of experts in pediatric infectious diseases, pediatric infectious diseases pharmacy, pediatric intensive care medicine, and pediatric hematology from 29 geographically diverse North American institutions was convened. Through a series of teleconferences and web-based surveys, a guidance statement was developed and refined based on review of the best available evidence and expert opinion. RESULTS: The course of COVID-19 in children and adolescents is typically mild and there is no high-quality evidence supporting any high-risk groups. There is no evidence for safety and efficacy of monoclonal antibody therapy for treatment of COVID-19 in children or adolescents, limited evidence of modest benefit in adults, and evidence for potential harm associated with infusion reactions or anaphylaxis. CONCLUSIONS: Based on evidence available as of December 20, 2020, the panel suggests against routine administration of monoclonal antibody therapy (bamlanivimab, or casirivimab and imdevimab), for treatment of COVID-19 in children or adolescents, including those designated by the FDA as at high risk of progression to hospitalization or severe disease. Clinicians and health systems choosing to use these agents on an individualized basis should consider risk factors supported by pediatric-specific evidence and ensure the implementation of a system for safe and timely administration that does not exacerbate existing healthcare disparities.

Healthcare worker perception of a global outbreak of novel coronavirus (COVID-19) and personal protective equipment: Survey of a pediatric tertiary-care hospital.

OBJECTIVE: In this study, we aimed to capture perspectives of healthcare workers (HCWs) on coronavirus disease 2019 (COVID-19) and infection prevention and control (IPAC) measures implemented during the early phase of the COVID-19 pandemic. DESIGN: A cross-sectional survey of HCWs. PARTICIPANTS: HCWs from the Hospital for Sick Children, Toronto, Canada. INTERVENTION: A self-administered survey was distributed to HCWs. We analyzed factors influencing HCW knowledge and self-reported use of personal protective equipment (PPE), concerns about contracting COVID-19 and acceptance of the recommended IPAC precautions for COVID-19. RESULTS: In total, 175 HCWs completed the survey between March 6 and March 10: 35 staff physicians (20%), 24 residents or fellows (14%), 72 nurses (41%), 14 respiratory therapists (8%), 14 administration staff (8%), and 14 other employees (8%). Most of the respondents were from the emergency department (n = 58, 33%) and the intensive care unit (n = 58, 33%). Only 86 respondents (50%) identified the correct donning order; only 60 (35%) identified the correct doffing order; but the majority (n = 113, 70%) indicated the need to wash their hands immediately prior to removal of their mask and eye protection. Also, 91 (54%) respondents felt comfortable with recommendations for droplet and/or contact precautions for routine care of patients with COVID-19. HCW occupation and concerns about contracting COVID-19 outside work were associated with nonacceptance of the recommendations (P = .016 and P = .036 respectively). CONCLUSION: As part of their pandemic response plans, healthcare institutions should have ongoing training for HCWs that focus on appropriate PPE doffing and discussions around modes of transmission of COVID-19.

Multicenter Interim Guidance on Use of Antivirals for Children With Coronavirus Disease 2019/Severe Acute Respiratory Syndrome Coronavirus 2.

BACKGROUND: Although coronavirus disease 2019 (COVID-19) is a mild infection in most children, a small proportion develop severe or critical illness. Data describing agents with potential antiviral activity continue to expand such that updated guidance is needed regarding use of these agents in children. METHODS: A panel of pediatric infectious diseases physicians and pharmacists from 20 geographically diverse North American institutions was convened. Through a series of teleconferences and web-based surveys, a set of guidance statements was developed and refined based on review of the best available evidence and expert opinion. RESULTS: Given the typically mild course of COVID-19 in children, supportive care alone is suggested for most cases. For children with severe illness, defined as a supplemental oxygen requirement without need for noninvasive or invasive mechanical ventilation or extracorporeal membrane oxygenation (ECMO), remdesivir is suggested, preferably as part of a clinical trial if available. Remdesivir should also be considered for critically ill children requiring invasive or noninvasive mechanical ventilation or ECMO. A duration of 5 days is appropriate for most patients. The panel recommends against the use of hydroxychloroquine or lopinavir-ritonavir (or other protease inhibitors) for COVID-19 in children. CONCLUSIONS: Antiviral therapy for COVID-19 is not necessary for the great majority of pediatric patients. For children with severe or critical disease, this guidance offers an approach for decision-making regarding use of remdesivir.

Respiratory syncytial virus prophylaxis for prevention of recurrent childhood wheeze and asthma: a systematic review.

BACKGROUND: Acute bronchiolitis caused by respiratory syncytial virus (RSV) has been associated with greater risk of recurrent wheezing and asthma. However, it is unclear whether this association is causal. RSV-specific monoclonal antibodies have been shown to reduce RSV-related hospitalisations in high-risk infants, but the longer-term follow-up has given conflicting evidence for prevention of recurrent wheeze or asthma. OBJECTIVE: We performed a systematic review and meta-analysis to determine whether monoclonal antibody prophylaxis against RSV bronchiolitis reduces the risk of subsequent recurrent wheeze or asthma. If so, this may support the hypothesis of causality. METHODS: Studies were identified via an online database search using Embase, MEDLINE, PubMed, Web of Science and the Cochrane Library. Manufacturers of monoclonal antibodies were contacted directly for unpublished data. The intervention of interest was RSV monoclonal antibody prophylaxis, and the primary outcome measure was recurrent wheeze and/or asthma. Studies were screened according to inclusion/exclusion criteria. Included studies were evaluated for quality and assessed for bias independently by 3 reviewers using the 'Grading of Recommendations Assessment, Development and Evaluation' (GRADE) approach. Results were extracted into 2 × 2 outcome tables and a meta-analysis carried out producing forest plots based on relative risk. Heterogeneity was assessed using the I2 statistic. RESULTS: The search identified 141 articles, which, after screening, resulted in eight studies (2 randomised controlled trials), thus including 11,195 infants in the meta-analysis. The overall result demonstrated a non-statistically significant reduction in relative risk of developing recurrent wheeze or asthma (RR 0.60; 95% CI 0.31 to 1.16). Study quality was generally low with evidence of publication bias and statistical heterogeneity. However, sub-group analysis excluding studies deemed to be 'very low' quality showed a relative risk of 0.42 (95% CI 0.22 to 0.80, p = 0.008). A further sub-group analysis for infants aged 32 to < 36 weeks showed a statistically significant relative risk of 0.35 (95% CI 0.14 to 0.86, p = 0.02). DISCUSSION: We did not identify an overall statistically significant benefit. However, our two sub-group analyses did find statistically significant benefits of monoclonal antibody therapy on the risk of recurrent wheeze and asthma. The main limitation of this study is the lack of high-quality randomised controlled trials, highlighting the need for more research in this field.

Visitor Restriction Policy on Pediatric Wards During Novel Coronavirus (COVID-19) Outbreak: A Survey Study Across North America.

Visitor restriction policies in pediatric wards during the novel coronavirus (COVID-19) outbreak are variable. Among 36 hospitals that responded to our survey, 97% allowed at least 1 visitor, with 67% restricting to 1 caregiver. Sixty-nine percent required the visitor to wear personal protective equipment and only 19% allowed non-household visitors.

Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide.

The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared on March 11, 2020 by the World Health Organization. As of the 31st of May, 2020, there have been more than 6 million COVID-19 cases diagnosed worldwide and over 370,000 deaths, according to Johns Hopkins. Thousands of SARS-CoV-2 strains have been sequenced to date, providing a valuable opportunity to investigate the evolution of the virus on a global scale. We performed a phylogenetic analysis of over 1,225 SARS-CoV-2 genomes spanning from late December 2019 to mid-March 2020. We identified a missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe (954 of 1,449 (66%) sequences) and is spreading worldwide (1,237 of 2,795 (44%) sequences). Molecular dating analysis estimated the emergence of this clade around mid-to-late January (10-25 January) 2020. We also applied structural bioinformatics to assess the potential impact of D614G on the virulence and epidemiology of SARS-CoV-2. In silico analyses on the spike protein structure suggests that the mutation is most likely neutral to protein function as it relates to its interaction with the human ACE2 receptor. The lack of clinical metadata available prevented our investigation of association between viral clade and disease severity phenotype. Future work that can leverage clinical outcome data with both viral and human genomic diversity is needed to monitor the pandemic.

Multicenter Initial Guidance on Use of Antivirals for Children With Coronavirus Disease 2019/Severe Acute Respiratory Syndrome Coronavirus 2.

BACKGROUND: Although coronavirus disease 2019 (COVID-19) is mild in nearly all children, a small proportion of pediatric patients develop severe or critical illness. Guidance is therefore needed regarding use of agents with potential activity against severe acute respiratory syndrome coronavirus 2 in pediatrics. METHODS: A panel of pediatric infectious diseases physicians and pharmacists from 18 geographically diverse North American institutions was convened. Through a series of teleconferences and web-based surveys, a set of guidance statements was developed and refined based on review of best available evidence and expert opinion. RESULTS: Given the typically mild course of pediatric COVID-19, supportive care alone is suggested for the overwhelming majority of cases. The panel suggests a decision-making framework for antiviral therapy that weighs risks and benefits based on disease severity as indicated by respiratory support needs, with consideration on a case-by-case basis of potential pediatric risk factors for disease progression. If an antiviral is used, the panel suggests remdesivir as the preferred agent. Hydroxychloroquine could be considered for patients who are not candidates for remdesivir or when remdesivir is not available. Antivirals should preferably be used as part of a clinical trial if available. CONCLUSIONS: Antiviral therapy for COVID-19 is not necessary for the great majority of pediatric patients. For those rare cases of severe or critical disease, this guidance offers an approach for decision-making regarding antivirals, informed by available data. As evidence continues to evolve rapidly, the need for updates to the guidance is anticipated.

Respiratory syncytial virus prophylaxis for prevention of recurrent childhood wheeze and asthma: a protocol for a systematic review.

BACKGROUND: Lower respiratory tract infection (LRTI) caused by respiratory syncytial virus (RSV) has been associated with greater risk of recurrent wheezing and subsequent asthma. However, it is still unclear whether this association is causal or not. RSV-specific monoclonal antibodies have been shown to reduce RSV-related hospitalisations in high-risk infants, i.e. those born pre-term, but the longer term follow-up has given conflicting evidence for the prevention of recurrent wheeze or asthma. OBJECTIVE: We aim to perform a systematic review and meta-analysis to determine whether or not prophylaxis with a monoclonal antibody for prevention of RSV-bronchiolitis reduces the risk of subsequent recurrent wheeze or asthma. If so, this would support the hypothesis that the association between RSV and recurrent wheeze and/or asthma is causative. METHODS: To identify relevant studies, we will search a number of databases including Medline, Embase, PubMed and Web of Science and will also manually look for unpublished data by contacting the manufacturers of monoclonal antibodies. The intervention being investigated is RSV-specific monoclonal antibody prophylaxis, and the outcome being measured is recurrent wheeze and/or asthma. Studies will be screened according to inclusion/exclusion criteria, to include primary studies of any study design type. Eligible studies will then be evaluated for quality and assessed for bias independently by three reviewers using the 'Grading of Recommendations Assessment, Development and Evaluation' (GRADE) approach. The results of the studies will be extracted into 2 × 2 outcome tables, and a meta-analysis will be carried out to produce forest plots based on relative risk. Heterogeneity will be assessed using the I 2 statistic. The statistical software we will use is StatsDirect. DISCUSSION: This review will aid in determining if the relationship between RSV and asthma development is a causal one, by showing the effect (if any) of RSV prophylaxis on subsequent recurrent wheeze/asthma. If this study shows RSV prophylaxis to have no effect on the outcome of recurrent wheeze/asthma, the question of causality remains.

Correction: Characterisation of morphological differences in well-differentiated nasal epithelial cell cultures from preterm and term infants at birth and one-year.

[This corrects the article DOI: 10.1371/journal.pone.0201328.].

Characterisation of morphological differences in well-differentiated nasal epithelial cell cultures from preterm and term infants at birth and one-year.

BACKGROUND: Innate immune responses of airway epithelium are important defences against respiratory pathogens and allergens. Newborn infants are at greater risk of severe respiratory infections compared to older infants, while premature infants are at greater risk than full term infants. However, very little is known regarding human neonatal airway epithelium immune responses and whether age-related morphological and/or innate immune changes contribute to the development of airway disease. METHODS: We collected nasal epithelial cells from 41 newborn infants (23 term, 18 preterm) within 5 days of birth. Repeat sampling was achieved for 24 infants (13 term, 11 preterm) at a median age of 12.5 months. Morphologically- and physiologically-authentic well-differentiated primary paediatric nasal epithelial cell (WD-PNEC) cultures were generated and characterised using light microscopy and immunofluorescence. RESULTS: WD-PNEC cultures were established for 15/23 (65%) term and 13/18 (72%) preterm samples at birth, and 9/13 (69%) term and 8/11 (73%) preterm samples at one-year. Newborn and infant WD-PNEC cultures demonstrated extensive cilia coverage, mucous production and tight junction integrity. Newborn WD-PNECs took significantly longer to reach full differentiation and were noted to have much greater proportions of goblet cells compared to one-year repeat WD-PNECs. No differences were evident in ciliated/goblet cell proportions between term- and preterm-derived WD-PNECs at birth or one-year old. CONCLUSION: We describe the successful generation of newborn-derived WD-PNEC cultures and their revival from frozen. We also compared the characteristics of WD-PNECs derived from infants born at term with those born prematurely at birth and at one-year-old. The development of WD-PNEC cultures from newborn infants provides a powerful and exciting opportunity to study the development of airway epithelium morphology, physiology, and innate immune responses to environmental or infectious insults from birth.