Epidemiological analysis of respiratory viral etiology for influenza-like illness during 2010 in Zhuhai, China

Characterising respiratory infections among hospitalised children during the COVID-19 pandemic in southeastern China: a cross-sectional study of pathogens and clinical association

OBJECTIVE

Children with acute respiratory tract infections (ARTIs) pose significantly burden on healthcare facilities due to high hospitalisation rates and mortality. However, limited epidemiological and clinical characteristics data on ARTIs in southeastern China during the COVID-19 pandemic exists.

DESIGN

Cross-sectional.

SETTING

Tertiary hospital associated with the First Affiliated Hospital, Fujian Medical University, China.

PARTICIPANTS

1007 hospitalised children diagnosed with ARTIs, aged 30 days to 15 years, were enrolled in this study from 1 January 2020 to 31 December 2021.

OUTCOME MEASURE

The primary outcomes are the rate of pathogen infections in children with ARTIs. Secondary outcomes are the description of risk factors associated with ARTIs in children.

RESULTS

Of the 1007 enrolled children, 28.2%, 42.2%, 21.8% and 7.7% were diagnosed with upper respiratory tract infection, bronchopneumonia, bronchitis and pneumonia, respectively. Mycoplasma pneumoniae (MP) was the most prevalent pathogen (31.9%), followed by influenza B virus (IFVB; 29.1%) and influenza A virus (IFVA; 19.1%). The study found that children under 1 year old (older than 30 days: ORIFVB=12.50; ORMP=8.53), children aged 1-3 years (ORMP=1.62), the winter season (ORIFVA=1.36), the time from symptoms onset to hospitalisation (ORMP=1.10) and increased precipitation (ORLP=1.01) were high-risk factors for ARTIs.

CONCLUSION

This investigation offers significant insights into the prevalence and distribution of common pathogens among children experiencing ARTIs in the context of the COVID-19 pandemic. The discernment of high-risk factors linked to these pathogens enhances our understanding of the epidemiological characteristics of ARTIs in children.

Epidemiology of Influenza-like Illness and Respiratory Viral Etiology in Adult Patients in Taiyuan City, Shanxi Province, China between 2018 and 2019

To determine the epidemiological status of influenza and understand the distribution of common respiratory viruses in adult patients with influenza-like illness (ILI) cases in Taiyuan City, Shanxi Province, China, epidemiological data between 2018 and 2019 were retrieved from the China Influenza Surveillance Information System, and two sentinel ILI surveillance hospitals were selected for sample collection. All specimens were screened for influenza virus (IFV) and the other 14 common respiratory viruses using real-time polymerase chain reaction. The results of the 2-year ILI surveillance showed that 26,205 (1.37%) of the 1,907,869 outpatients and emergency patients presented with ILI, with an average annual incidence of 297.75 per 100,000 individuals, and ILI cases were predominant in children <15 years (21,348 patients, 81.47%). Of the 2713 specimens collected from adult patients with ILI, the overall detection rate of respiratory viruses was 20.13%, with IFV being the most frequently detected (11.79%) and at a relatively lower rate than other respiratory viruses. Further subtype analysis indicated an alternating or mixed prevalence of H1N1 (2009), H3N2, Victoria, and Yamagata subtypes. This study provides a baseline epidemiological characterization of ILI and highlights the need for a nationwide detection and surveillance system for multiple respiratory pathogens.

Spatiotemporal effects of meteorological conditions on global influenza peaks

BACKGROUND

Numerous studies have suggested that meteorological conditions such as temperature and absolute humidity are highly indicative of influenza outbreaks. However, the explanatory power of meteorological factors on the seasonal influenza peaks varied widely between countries at different latitudes.

OBJECTIVES

We aimed to explore the modification effects of meteorological factors on the seasonal influenza peaks in multi-countries.

METHODS

Data on influenza positive rate (IPR) were collected across 57 countries and data on meteorological factors were collected from ECMWF Reanalysis v5 (ERA5). We used linear regression and generalized additive models to investigate the spatiotemporal associations between meteorological conditions and influenza peaks in cold and warm seasons.

RESULTS

Influenza peaks were significantly correlated with months with both lower and higher temperatures. In temperate countries, the average intensity of cold season peaks was stronger than that of warm season peaks. However, the average intensity of warm season peaks was stronfger than of cold season peaks in tropical countries. Temperature and specific humidity had synergistic effects on influenza peaks at different latitudes, stronger in temperate countries (cold season: R2=0.90; warm season: R2=0.84) and weaker in tropical countries (cold season: R2=0.64; warm season: R2=0.03). Furthermore, the effects could be divided into cold-dry and warm-humid modes. The temperature transition threshold between the two modes was 16.5-19.5 °C. During the transition from cold-dry mode to warm-humid mode, the average 2 m specific humidity increased by 2.15 times, illustrating that transporting a large amount of water vapor may compensate for the negative effect of rising temperatures on the spread of the influenza virus.

CONCLUSION

Differences in the global influenza peaks were related to the synergistic influence of temperature and specific humidity. The global influenza peaks could be divided into cold-dry and warm-humid modes, and specific thresholds of meteorological conditions were needed for the transition of the two modes.

Characterization of T Helper 1 and 2 Cytokine Profiles in Newborns of Mothers with COVID-19

An infectious disease caused by SARS-CoV-2, COVID-19 greatly affects the pediatric population and is 3 times more prevalent in newborns than in the general population. In newborns, the overexpression of immunological molecules may also induce a so-called cytokine storm. In our study, we evaluated the expression of cytokines in newborns admitted to a neonatal ICU whose mothers had SARS-CoV-2 and symptoms of SARS. The blood of newborns of infected and healthy mothers was collected to identify their Th1 and Th2 cytokine profiles, and via flow cytometry, the cytokines TNF-α, IFN-γ, IL-2, IL-6, and IL-10 were identified. Overexpression was observed in the Th1 and Th2 cytokine profiles of newborns from infected mothers compared with the control group. Statistical analysis also revealed significant differences between the cellular and humoral responses of the infected group versus the control group. The cellular versus humoral responses of the newborns of infected mothers were also compared, which revealed the prevalence of the cellular immune response. These data demonstrate that some cytokines identified relate to more severe symptoms and even some comorbidities. IL-6, TNF-α, and IL-10 may especially be related to cytokine storms in neonates of mothers with COVID-19.

Distinguishing viruses responsible for influenza-like illness

The many respiratory viruses that cause influenza-like illness (ILI) are reported and tracked as one entity, defined by the CDC as a group of symptoms that include a fever of 100 degrees Fahrenheit, a cough, and/or a sore throat. In the United States alone, ILI impacts 9-49 million people every year. While tracking ILI as a single clinical syndrome is informative in many respects, the underlying viruses differ in parameters and outbreak properties. Most existing models treat either a single respiratory virus or ILI as a whole. However, there is a need for models capable of comparing several individual viruses that cause respiratory illness, including ILI. To address this need, here we present a flexible model and simulations of epidemics for influenza, RSV, rhinovirus, seasonal coronavirus, adenovirus, and SARS/MERS, parameterized by a systematic literature review and accompanied by a global sensitivity analysis. We find that for these biological causes of ILI, their parameter values, timing, prevalence, and proportional contributions differ substantially. These results demonstrate that distinguishing the viruses that cause ILI will be an important aspect of future work on diagnostics, mitigation, modeling, and preparation for future pandemics.

Hospital utilization rates for influenza and RSV: a novel approach and critical assessment

BACKGROUND

Influenza and respiratory syncytial virus (RSV) contribute significantly to the burden of acute lower respiratory infection (ALRI) inpatient care, but heterogeneous coding practices and availability of inpatient data make it difficult to estimate global hospital utilization for either disease based on coded diagnoses alone.

METHODS

This study estimates rates of influenza and RSV hospitalization by calculating the proportion of ALRI due to influenza and RSV and applying this proportion to inpatient admissions with ALRI coded as primary diagnosis. Proportions of ALRI attributed to influenza and RSV were extracted from a meta-analysis of 360 total sources describing inpatient hospital admissions which were input to a Bayesian mixed effects model over age with random effects over location. Results of this model were applied to inpatient admission datasets for 44 countries to produce rates of hospital utilization for influenza and RSV respectively, and rates were compared to raw coded admissions for each disease.

RESULTS

For most age groups, these methods estimated a higher national admission rate than the rate of directly coded influenza or RSV admissions in the same inpatient sources. In many inpatient sources, International Classification of Disease (ICD) coding detail was insufficient to estimate RSV burden directly. The influenza inpatient burden estimates in older adults appear to be substantially underestimated using this method on primary diagnoses alone. Application of the mixed effects model reduced heterogeneity between countries in influenza and RSV which was biased by coding practices and between-country variation.

CONCLUSIONS

This new method presents the opportunity of estimating hospital utilization rates for influenza and RSV using a wide range of clinical databases. Estimates generally seem promising for influenza and RSV associated hospitalization, but influenza estimates from primary diagnosis seem highly underestimated among older adults. Considerable heterogeneity remains between countries in ALRI coding (i.e., primary vs non-primary cause), and in the age profile of proportion positive for influenza and RSV across studies. While this analysis is interesting because of its wide data utilization and applicability in locations without laboratory-confirmed admission data, understanding the sources of variability and data quality will be essential in future applications of these methods.

Lessons from healthcare personnel screening and management during H1N1 pandemic in preparation for the impending COVID-19 pandemic in a tertiary care hospital in India

Background

In the wake of the COVID-19 pandemic caused by a novel corona virus, health care personnel are at increased risk of acquiring the infection. In preparation for the management of health care personnel that are likely to be infected, we looked in to the data collected during the Influenza pandemic in 2009, caused by a novel strain of H1N1 influenza called swine flu. The care of healthcare personnel in our institution, who had an acute febrile respiratory illness (AFRI) during that period was routed through a single channel using a uniform protocol. We retrospectively analysed the available data, during the initial four months of the pandemic, to draw lessons from it.

Objective

To study the prevalence, clinical profile and risk factors of swine flu among health care personnel during the pandemic of 2009 in a tertiary care hospital in South India.

Methodology

This retrospective study enrolled all the health care personnel including students of a tertiary care institution in South India, who presented with an AFRI between June to August, the initial four months of the swine flu pandemic of 2009. The clinical profile and risk factors were extracted. The results of the RT PCR for swine flu was obtained. Prevalence in each demographic group was calculated and compared. Characteristics of those with swine flu were compared with those who turned negative for the swine flu.

Results

The prevalence of all AFRI and only swine flu among health care personnel during the study period was 18 per thousand and 8.7 per thousand respectively. Highest prevalence of swine flu was found among students and office staff. After adjusting for confounding factors, hyperthermia at presentation was significantly higher {OR = 1.97; 95% CI (1.01–3.76)} among those who tested positive for swine flu as compared with those with other AFRI's. Only 2.5% of the entire AFRI group required admission and there was no mortality.

Conclusion

Health care personnel are at increased risk of acquiring infection. Our study demonstrated that students and office staff were the most susceptible. Unprotected exposure to unknown infectious patients and relatives is likely to have been an important factor. Though the mode of transmission is similar, compared to H1N1, COVID-19 is associated with different comorbidities and has significantly higher mortality. Therefore, in preparation for the COVID-19 pandemic, the personal protective equipment of the healthcare personnel need to be escalated.

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During a pandemic, health care personnel are at increased risk of acquiring infection.

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Unprotected exposure to unknown infectious patients is an important factor for transmission.

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Compared to H1N1, COVID-19 is associated with different comorbidities and has significantly higher mortality.

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In preparation for the COVID-19 pandemic, the personal protective equipment of the healthcare personnel need to be escalated.

Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania

Upper-respiratory tract infections (URTI) are the leading causes of childhood morbidities. This study investigated etiologies and patterns of URTI among children in Mwanza, Tanzania. A cross-sectional study involving 339 children was conducted between October-2017 and February-2018. Children with features suggestive of URTI such as nasal congestion, dry cough, painful swallowing and nasal discharge with/without fever were enrolled. Pathogens were detected from nasopharyngeal and ear-swabs by multiplex-PCR and culture respectively. Full blood count and C-reactive protein analysis were also done. The median age was 16 (IQR: 8-34) months. Majority (82.3%) had fever and nasal-congestion (65.5%). Rhinitis (55.9%) was the commonest diagnosis followed by pharyngitis (19.5%). Viruses were isolated in 46% of children, the commonest being Rhinoviruses (23.9%). Nineteen percent of children had more than 2 viruses; Rhinovirus and Enterovirus being the commonest combination. The commonest bacteria isolated from ears were Staphylococcus aureus and Pseudomonas aeruginosa. Children with viral pathogens had significantly right shift of lymphocytes (73%-sensitivity). Majority (257/339) of children were symptoms free on eighth day. Viruses are the commonest cause of URTI with Rhinitis being the common diagnosis. Rapid diagnostic assays for URTI pathogens are urgently needed in low-income countries to reduce unnecessary antibiotic prescriptions which is associated with antibiotic resistance.

Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness

Influenza-like illness (ILI) is a commonly measured syndromic signal representative of a range of acute respiratory infections. Reliable forecasts of ILI can support better preparation for patient surges in healthcare systems. Although ILI is an amalgamation of multiple pathogens with variable seasonal phasing and attack rates, most existing process-based forecasting systems treat ILI as a single infectious agent. Here, using ILI records and virologic surveillance data, we show that ILI signal can be disaggregated into distinct viral components. We generate separate predictions for six contributing pathogens (influenza A/H1, A/H3, B, respiratory syncytial virus, and human parainfluenza virus types 1-2 and 3), and develop a method to forecast ILI by aggregating these predictions. The relative contribution of each pathogen to the total ILI signal is estimated using a Markov Chain Monte Carlo (MCMC) method upon forecast aggregation. We find highly variable overall contributions from influenza type A viruses across seasons, but relatively stable contributions for the other pathogens. Using historical data from 1997 to 2014 at US national and regional levels, the proposed forecasting system generates improved predictions of both seasonal and near-term targets relative to a baseline method that simulates ILI as a single pathogen. The hierarchical forecasting system can generate predictions for each viral component, as well as infer and predict their contributions to ILI, which may additionally help physicians determine the etiological causes of ILI in clinical settings.

The burden of respiratory syncytial virus in adults: a systematic review and meta-analysis

Respiratory syncytial virus (RSV) is the most common pathogen associated with acute lower respiratory tract infections in young children. RSV is also a major viral pathogen causing severe lung disease in the adult population, particularly among the elderly. We conducted a review of adult RSV studies published from January 1970 to February 2017 to determine the burden of disease among adults worldwide. There were no restrictions on health care setting or definition of RSV infection. A total of 1530 published studies were identified, 95 of which were included in this review. The incidence rates of hospitalised RSV acute respiratory tract infection (ARI) in adults >65 years old ranged from 7.3 to 13.0/10⁵ population in Africa and Asia and from 190 to 254/10⁵ population in the USA. Higher incidence rates (195–1790/10⁵ population) were observed in adults ≥50 years old for outpatient or emergency visits in the USA. Of all ARI patients, RSV accounted for 1–10% in adults and 2–14% in patients with chronic diseases or transplantation. Given the limitations in the existing data, significant efforts should be made to generate evidence on the burden of RSV infections in adults and to estimate the potential impact of future preventive interventions.

Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China

Background

This study aims to describe the epidemiological patterns of influenza-like illness (ILI) in Huludao, China and seek scientific evidence on the link of ILI activity with weather factors.

Methods

Surveillance data of ILI cases between January 2012 and December 2015 was collected in Huludao Central Hospital, meteorological data was obtained from the China Meteorological Data Service Center. Generalized additive model (GAM) was used to seek the relationship between the number of ILI cases and the meteorological factors. Multiple Smoothing parameter estimation was made on the basis of Poisson distribution, where the number of weekly ILI cases was treated as response, and the smoothness of weather was treated as covariates. Lag time was determined by the smallest Akaike information criterion (AIC). Smoothing coefficients were estimated for the prediction of the number of ILI cases.

Results

A total of 29, 622 ILI cases were observed during the study period, with children ILI cases constituted 86.77%. The association between ILI activity and meteorological factors varied across different lag periods. The lag time for average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity were 2, 2, 1, 1 and 0 weeks, respectively. Average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity could explain 16.5%, 9.5%, 18.0%, 15.9% and 7.7% of the deviance, respectively. Among the temperature indexes, the minimum temperature played the most important role. The number of ILI cases peaked when minimum temperature was around -13 °C in winter and 18 °C in summer. The number of cases peaked when the relative humidity was equal to 43% and then began to decrease with the increase of relative humidity. When the humidity exceeded 76%, the number of ILI cases began to rise.

Conclusions

The present study first analyzed the relationship between meteorological factors and ILI cases with special consideration of the length of lag period in Huludao, China. Low air temperature and low relative humidity (cold and dry weather condition) played a considerable role in the epidemic pattern of ILI cases. The trend of ILI activity could be possibly predicted by the variation of meteorological factors.

The epidemiology and severity of respiratory viral infections in a tropical country: Ecuador, 2009-2016

BACKGROUND

Respiratory viral infections (RVI) are a leading cause of mortality worldwide. We compared the epidemiology and severity of RVI in Ecuador during 2009-2016.

METHODS

Respiratory specimens collected within the national surveillance system were tested for influenza viruses, respiratory syncytial virus (RSV), adenovirus, parainfluenza virus, and human metapneumovirus. Overall and virus-specific positive detection rate (PDR) were calculated and compared the timing of epidemics caused by the different viruses. Logistic regression models were used to compare the age distribution and risk of death across respiratory viruses.

RESULTS

A total of 41,172 specimens were analyzed: influenza (PDR=14.3%) and respiratory syncytial virus (RSV) (PDR=9.5%) were the most frequently detected viruses. Influenza epidemics typically peaked in December-January and RSV epidemics in March; seasonality was less evident for the other viruses. Compared to adults, children were more frequently infected with RSV, adenovirus, parainfluenza, and influenza B, while the elderly were less frequently infected with influenza A(H1N1)p. The age-adjusted risk of death was highest for A(H1N1)p (odds ratio [OR] 1.73, 95% confidence intervals [CI] 1.38-2.17), and lowest for RSV (OR 0.75, 95%CI 0.57-0.98).

CONCLUSIONS

Whilst influenza and RSV were the most frequently detected pathogens, the risk of death differed by RVI, being highest for pandemic influenza and lowest for RSV.

Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 - 2017)

Background

Acute respiratory infections (ARIs) cause a considerable morbidity and mortality worldwide especially in children. However, there are few studies of the etiological structure of ARIs in Russia. In this work, we analyzed the etiology of ARIs in children (0–15 years old) admitted to Novosibirsk Children’s Municipal Clinical Hospital in 2013–2017.

Methods

We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit.

Results

We detected 1128 (72.3%) samples were positive for at least one virus. The most frequently detected pathogens were respiratory syncytial virus (358/1560, 23.0%), influenza virus (344/1560, 22.1%), and rhinovirus (235/1560, 15.1%). Viral co-infections were found in 163 out of the 1128 (14.5%) positive samples. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses.

Conclusions

We evaluated the distribution of respiratory viruses in children with ARIs and showed the prevalence of respiratory syncytial virus and influenza virus in the etiological structure of infections. This study is important for the improvement and optimization of diagnostic tactics, control and prevention of the respiratory viral infections.

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.

Literature review of the epidemiology of influenza B disease in 15 countries in the Asia-Pacific region

Influenza control strategies focus on the use of trivalent influenza vaccines containing two influenza A virus subtypes and one of the two circulating influenza type B lineages (Yamagata or Victoria). Mismatches between the vaccine B lineage and the circulating lineage have been regularly documented in many countries, including those in the Asia‐Pacific region. We conducted a literature review with the aim of understanding the relative circulation of influenza B viruses in Asia‐Pacific countries. PubMed and Western Pacific Region Index Medicus were searched for relevant articles on influenza type B published since 1990 in English language for 15 Asia‐Pacific countries. Gray literature was also accessed. From 4834 articles identified, 121 full‐text articles were analyzed. Influenza was reported as an important cause of morbidity in the Asia‐Pacific region, affecting all age groups. In all 15 countries, influenza B was identified and associated with between 0% and 92% of laboratory‐confirmed influenza cases in any one season/year. Influenza type B appeared to cause more illness in children aged between 1 and 10 years than in other age groups. Epidemiological data for the two circulating influenza type B lineages remain limited in several countries in the Asia‐Pacific, although the co‐circulation of both lineages was seen in countries where strain surveillance data were available. Mismatches between circulating B lineages and vaccine strains were observed in all countries with available data. The data suggest that a shift from trivalent to quadrivalent seasonal influenza vaccines could provide additional benefits by providing broader protection.

Viruses causing severe acute respiratory infections (SARI) in children ≤5 years of age at a tertiary care hospital in Rajasthan, India

BACKGROUND & OBJECTIVES

Severe acute respiratory infection (SARI) is one of the leading causes of death among children worldwide. As different respiratory viruses exhibit similar symptoms, simultaneous detection of these viruses in a single reaction mixture can save time and cost. The present study was done in a tertiary care children's hospital for rapid identification of viruses causing SARI among children less than or equal to five years of age using multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) kit.

METHODS

A total of 155 throat swabs were collected from equal number of children suspected to have SARI and processed for extraction of nucleic acids using automated extraction system. Multiplex real-time RT-PCR was done to identify the viruses in the samples.

RESULTS

The overall positivity for viruses in the study was found to be 72.9 per cent with a co-infection rate of 19.5 per cent. Human metapneumovirus (HMPV) was the predominant virus detected in 25.7 per cent children followed by influenza A (H1N1)pdm09, human rhinovirus (HRV) and human adenovirus (HAdV) in 19.9, 11.0 and 8.8 per cent children, respectively. The HMPV was at its peak in February 2013, HAdV showed two peaks in March-April, 2012 and November 2012-March 2013 while HRV was detected throughout the year.

INTERPRETATION & CONCLUSIONS

Multiplex real-time PCR helped in rapid identification of viruses. Seventeen viruses were detected in SARI cases with overall positivity of 72.9 per cent. HMPV was the most predominant virus. However, for better clinico-virological correlation, studies are required with complete work up of all the aetiological agents, clinical profile of patients and treatment outcome.

Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses

Background

Human adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases.

Methodology and results

From January 2012 to December 2015 swabs were collected from consenting ILI outpatients. Adenoviral detection is performed by rRT-PCR with the Anyplex^™ II RV16 Detection kit (Seegene) and molecular characterization was performed using a partial hexon gene sequence. 6381 samples were collected. More than half of patients (51.7%; 3297/6381) were children of ≤ 5 years. 1967 (30.8%) were positive for HAdV with 1561 (79.4%) found in co-infection with at least one another respiratory virus. The most common co-detections were with influenza viruses (53.1%; 1045/1967), rhinoviruses (30%; 591/1967), enteroviruses (18.5%; 364/1967) and RSV (13.5%; 266/1967). Children under 5 were the most infected group (62.2%; 1224/1967; p <0.05). We noted that HAdV was detected throughout the year at a high level with detection peaks of different amplitudes without any clear seasonality. Phylogenetic analysis revealed species HAdV-C in majority, species HAdV-B and one HAdV- 4 genome type. The 9 HAdV-B species like strains from Senegal grouped with genome types HAdV-7, HAdV-55 and HAdV-11 as shown by a phylogenetic branch with a high bootstrap value of (88%).

Conclusion

In conclusion, the results of the present study suggest strong year-round HAdV activity in Senegal, especially in children up to 5 years of age. Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B species. The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections.

Epidemiologic Analysis of Respiratory Viral Infections Mainly in Hospitalized Children and Adults in a Midwest University Medical Center After the Implementation of a 14-Virus Multiplex Nucleic Acid Amplification Test

OBJECTIVES

To investigate the etiology of viral respiratory tract infections mainly in hospitalized children and adults over a 12-month consecutive period after implementation of a 14-virus multiplex nucleic acid amplification test.

METHODS

From January 2014 to January 2015, a total of 2,237 respiratory samples were analyzed with the US Food and Drug Administration-cleared eSensor Respiratory Viral Panel (GenMark Diagnostics, Carlsbad, CA).

RESULTS

Of the 2,237 specimens tested, 788 specimens were positive for at least one virus, giving a positivity rate of 35.2%, and because of viral codetection, a total of 862 viral targets were identified. The age groups with the highest positivity rates were the 0- to 1-year (73.5%) and 2- to 6-year (78.4%) age groups. The overall viral codetection rate was 9.1%. Human rhinovirus (HRV) was the most prevalent respiratory virus found in children and adults. The peak of HRV seen in September 2014 represented a combination of HRV and enterovirus D68, 2014 epidemic respiratory infections.

CONCLUSION

The ability to detect a wider range of respiratory viruses gave us a better understanding of the etiology of respiratory infections in our population, particularly for HRV and enhanced our ability to detect viral coinfection.

Epidemiological and clinical characteristics of respiratory viral infections in children in Shanghai, China

Acute respiratory tract infections (ARTIs) due to various viruses are not only the most common causes of upper and lower respiratory infection but are also major causes of morbidity and mortality in children. In this study, we investigated the prevalence and clinical characteristics of children with virus-related ARTIs and determined the spectrum of respiratory viruses and their correlation with meteorological variables in Jiading District, Shanghai, China. Nasopharyngeal swabs from 2819 children with ARTIs were collected from August 2011 to December 2014, and used for detection of respiratory viruses by multiplex RT-PCR. Seventeen respiratory viruses were detected among 691 (24.5 %) of 2819 patients. The highest prevalence of respiratory viruses was detected in the age group of less than 1 year (29.0 %), and the prevalence decreased with age. This suggests that children less than one year old are the most susceptible to infection. Influenza virus (IFV) was the most frequently detected virus (5.8 %), followed by parainfluenza virus (PIV) (5.7 %), enterovirus (EV) (4.3 %), and respiratory syncytial virus (RSV) (3.6 %). Statistical analysis showed that epidemics of IFV, PIV and EV had distinct seasonal variations. Mean monthly temperature appeared to be the only meteorological factor associated with IFV and PIV infection. These findings will provide valuable information for decision-making, prevention and treatment of ARTIs in children.

Viral etiology of medically attended influenza-like illnesses in children less than five years old in Suzhou, China, 2011-2014

Limited information is available on the non‐influenza etiology and epidemiology of influenza‐like illness (ILI) in China. From April 2011 to March 2014, we collected oropharyngeal swabs from children less than 5 years of age with symptoms of ILI who presented to the outpatient departments of Suzhou University Affiliated Children's Hospital (SCH). We used reverse transcription polymerase chain reaction (rt‐PCR) or PCR to detect 11 respiratory viruses. Among 3,662 enrolled ILI patients, 1,292 (35.3%) tested positive for at least one virus. Influenza virus (16.9%) was detected most frequently (influenza A 7.4%, influenza B 9.5%), followed by respiratory syncytial virus (RSV) (5.6%), parainfluenza virus (PIV) types 1–4 (4.8%), human bocavirus (HBoV) (3.8%), human metapneumovirus (HMPV) (3.5%), and adenovirus (ADV) (3.0%). Co‐infections were identified in 108 (2.9%) patients. Influenza virus predominantly circulated in January–March and June–July. The 2013–2014 winter peaks of RSV and influenza overlapped. Compared with other virus positive cases, influenza positive cases were more likely to present with febrile seizure, and RSV positive cases were more likely to present with cough and wheezing, and were most frequently diagnosed with pneumonia. These data provide a better understanding of the viral etiology of ILI among children less than 5 years of age in Suzhou, China. Influenza is not only the most frequently identified pathogen but it is also the only vaccine preventable illness among the 11 pathogens tested. Such findings suggest the potential value of exploring value of influenza vaccination among this influenza vaccination target group. J. Med. Virol. 88:1334–1340, 2016. © 2016 Wiley Periodicals, Inc.

The clinical and etiological characteristics of influenza-like illness (ILI) in outpatients in Shanghai, China, 2011 to 2013

INTRODUCTION

Clinical and etiological characteristics of influenza-like illness (ILI) in outpatients is poorly understood in the southern temperate region of China. We conducted laboratory-based surveillance of viral etiology for ILI outpatients in Shanghai from January 2011 to December 2013.

MATERIALS AND METHODS

Clinical and epidemiological data from ILI outpatients, both children and adults, were collected. A total of 1970 nasopharyngeal swabs were collected and tested for 12 respiratory viruses using multiplex RT-PCR, and the data were analyzed anonymously.

RESULTS

All 12 respiratory viruses were detected in the specimens. At least one virus was detected in 32.4% of 1970 specimens analyzed, with 1.1% showing co-infections. The most frequently detected agents were influenza A (11.7%), influenza B (9.6%), and rhinoviruses (3.1%).Other viruses were present at a frequency less than 3.0%. We observed a winter peak in the detection rate in ILI patients during 3 years of surveillance and a summer peak in 2012. HCoV, HADV, and HMPV were detected more frequently in children than in adults. Patients infected with influenza virus experienced higher temperatures, more coughs, running noses, headaches and fatigue than patients infected with other viruses and virus-free patients (p<0.001).

CONCLUSIONS

The spectrum, seasonality, age distribution and clinical associations of respiratory virus infections in children and adults with influenza-like illness were analyzed in this study for the first time. To a certain extent, the findings can provide baseline data for evaluating the burden of respiratory virus infection in children and adults in Shanghai. It will also provide clinicians with helpful information about the etiological patterns of outpatients presenting with complaints of acute respiratory syndrome, but further studies should be conducted, and longer-term laboratory-based surveillance would give a better picture of the etiology of ILI.

Technical guidelines for the application of seasonal influenza vaccine in China (2014-2015)

Influenza, caused by the influenza virus, is a respiratory infectious disease that can severely affect human health. Influenza viruses undergo frequent antigenic changes, thus could spread quickly. Influenza causes seasonal epidemics and outbreaks in public gatherings such as schools, kindergartens, and nursing homes. Certain populations are at risk for severe illness from influenza, including pregnant women, young children, the elderly, and people in any ages with certain chronic diseases.

Epidemiology of pathogen-specific respiratory infections among three US populations

BACKGROUND

Diagnostic tests for respiratory infections can be costly and time-consuming. Improved characterization of specific respiratory pathogens by identifying frequent signs, symptoms and demographic characteristics, along with improving our understanding of coinfection rates and seasonality, may improve treatment and prevention measures.

METHODS

Febrile respiratory illness (FRI) and severe acute respiratory infection (SARI) surveillance was conducted from October 2011 through March 2013 among three US populations: civilians near the US-Mexico border, Department of Defense (DoD) beneficiaries, and military recruits. Clinical and demographic questionnaire data and respiratory swabs were collected from participants, tested by PCR for nine different respiratory pathogens and summarized. Age stratified characteristics of civilians positive for influenza and recruits positive for rhinovirus were compared to other and no/unknown pathogen. Seasonality and coinfection rates were also described.

RESULTS

A total of 1444 patients met the FRI or SARI case definition and were enrolled in this study. Influenza signs and symptoms varied across age groups of civilians. Recruits with rhinovirus had higher percentages of pneumonia, cough, shortness of breath, congestion, cough, less fever and longer time to seeking care and were more likely to be male compared to those in the no/unknown pathogen group. Coinfections were found in 6% of all FRI/SARI cases tested and were most frequently seen among children and with rhinovirus infections. Clear seasonal trends were identified for influenza, rhinovirus, and respiratory syncytial virus.

CONCLUSIONS

The age-stratified clinical characteristics associated with influenza suggest that age-specific case definitions may improve influenza surveillance and identification. Improving identification of rhinoviruses, the most frequent respiratory infection among recruits, may be useful for separating out contagious individuals, especially when larger outbreaks occur. Overall, describing the epidemiology of pathogen specific respiratory diseases can help improve clinical diagnoses, establish baselines of infection, identify outbreaks, and help prioritize the development of new vaccines and treatments.

The influence of diurnal temperature range on the incidence of respiratory syncytial virus in Japan

The incidence of respiratory syncytial virus (RSV) has been reported to exhibit seasonal variation. However, the impact of diurnal temperature range (DTR) on RSV has not been investigated. After acquiring data related to cases of RSV and weather parameters of DTR in Fukuoka, Japan, between 2006 and 2012, we used negative binomial generalized linear models and distributed lag nonlinear models to assess the possible relationship between DTR and RSV cases, adjusting for confounding factors. Our analysis revealed that the weekly number of RSV cases increased with a relative risk of 3·30 (95% confidence interval 1·65-6·60) for every 1°C increase in DTR. Our study provides quantitative evidence that the number of RSV cases increased significantly with increasing DTR. We suggest that preventive measures for limiting the spread of RSV should be considered during extended periods of high DTR.

Is influenza-like illness a useful concept and an appropriate test of influenza vaccine effectiveness?

PURPOSE

To assess the utility of "influenza-like illness" (ILI) and whether it appropriately tests influenza vaccine effectiveness.

PRINCIPAL RESULTS

The WHO and CDC definitions of "influenza-like illness" are similar. However many studies use other definitions, some not specifying a temperature and requiring specific respiratory and/or systemic symptoms, making many samples non-comparable. Most ILI studies find less than 25% of cases are RT-PCR-positive, those which test for other viruses and bacteria usually find multiple other pathogens, and most identify no pathogen in about 50% of cases. ILI symptom and symptom combinations do not have high sensitivity or specificity in identifying PCR-positive influenza cases. Rapid influenza diagnostic tests are increasingly used to screen ILI cases and they have low sensitivity and high specificity when compared to RT-PCR in identifying influenza.

MAIN CONCLUSIONS

The working diagnosis of ILI presumes influenza may be involved until proven otherwise. Health care workers would benefit by renaming the WHO and CDC ILI symptoms and signs as "acute respiratory illness" and also using the WHO acute severe respiratory illness definition if the illness is severe and meets this criterion. This renaming would shift attention to identify the viral and bacterial pathogens in cases and epidemics, identify new pathogens, implement vaccination plans appropriate to the identified pathogens, and estimate workload during the viral season. Randomised controlled trials testing the effectiveness of influenza vaccine require all participants to be assessed by a gold standard (RT-PCR). ILI has no role in measuring influenza vaccine effectiveness. ILI is well established in the literature and in the operational definition of many surveillance databases and its imprecise definition may be inhibiting progress in research and treatment. The current ILI definition could with benefit be renamed "acute respiratory illness," with additional definitions for "severe acute respiratory illness" (SARI) with RT-PCR testing for pathogens to facilitate prevention and treatment.

Viral etiology of influenza-like illnesses in Huizhou, China, from 2011 to 2013

Little information is available on the etiology and prevalence of viruses other than influenza viruses causing influenza-like illnesses (ILIs) in China. This study was conducted for simultaneous detection and identification of 14 respiratory viruses in Huizhou using real-time PCR. In total, viruses were detected in 48.66 % of ILI patient samples, in which influenza virus (19.98 %) was the most commonly detected, followed by rhinovirus (7.46 %), human coronaviruses (3.63 %), human metapneumovirus (3.06 %), parainfluenza virus (3.06 %), respiratory syncytial virus (2.39 %), adenovirus (2.29 %), and human bocavirus (1.43 %). Co-infections occurred in 5.35 % of all tested specimens and 11.00 % (56/509) of infected patients. Children under 5 years and adults older than 60 years were more likely to have one or more detectable viruses associated with their ILI (OR=1.75, 95 % CI: 1.37; 2.23). Influenza virus was detected during each month of each year, and increased viral activity was observed in 2013. Infections with adenovirus and human metapneumovirus had characteristic seasonal patterns. No significant differences were found in positive the rate between the gender groups, while significantly differences in positive rate were found among the different age groups (P-value<0.001). This study confirmed that multiple respiratory viruses may circulate concurrently in the population and play an important role in the etiology of ILI. The most frequent symptoms associated with respiratory viruses were sore throat, rhinorrhea and headache. This information needs to be considered by clinicians when treating patients presenting with ILI, and it could serve as a reference for government officers when designing and implementing effective intervention plans.

Molecular analysis of human metapneumovirus detected in patients with lower respiratory tract infection in upper egypt

Introduction. Since 2001, when Human metapneumovirus (HMPV) was isolated in the Netherlands, the virus has been detected in several continents. Although reports have confirmed the prevalence of HMPV worldwide, data from Egypt remain limited. HMPV plays an important role in respiratory tract infections in individuals of all ages particularly in children. This study was aimed at estimating the prevalence of HMPV in patients with community-acquired lower respiratory infection in Upper Egypt and characterizing the circulating Egyptian HMPV strains for the first time. Materials and Methods. From 2005 to 2008, respiratory samples from 520 patients were analyzed for the presence of HMPV by real-time RT-PCR. Molecular and phylogenetic analyses were performed on partial fusion gene sequences of HMPV-positive patients. Results. HMPV-positive patients were detected in 2007-2008. The overall infection rate was 4%, while 57% of the patients were children. Sequence analysis demonstrated circulation of subgroup B viruses with predominance of lineage B2. Nucleotide sequence identity within lineage B1 was 98.8%–99.7% and higher than that in lineage B2 (94.3%–100%). Three new amino acid substitutions (T223N, R229K, and D280N) of lineage B2 were observed. Conclusion. HMPV is a major viral pathogen in the Egyptian population especially in children. During 2007-2008, predominantly HMPV B2 circulated in Upper Egypt.