Viral etiology of severe pneumonia among Kenyan infants and children

Pattern of Viral Infections among Infants and Children Admitted to the Paediatric Intensive Care Unit at Sultan Qaboos University Hospital, Oman

OBJECTIVES

The aim of this study was to describe the pattern of viral infections in infants and children admitted to the Paediatric Intensive Care Unit (PICU) at Sultan Qaboos University Hospital (SQUH) in Muscat, Oman.

METHODS

A retrospective review of patient records was carried out on all patients admitted to the PICU between January 2011 and December 2012. In order to detect viruses, polymerase chain reaction (PCR) technology was used to detect viruses in nasopharyngeal aspirates, tracheal aspirates, plasma, stool and urine samples. All infants and children below 13 years old, who were admitted to the PICU at SQUH during the study period and with confirmed viral infections, were included in the study.

RESULTS

A total of 373 infants and children were admitted to the PICU during the study period. Viruses were detected in 34 patients. The most frequently detected viruses were cytomegalovirus (CMV) in 29.4%; this virus was noted predominantly in immuncompromised patients (80%, P = 0.023) and was associated with increased mortality (50%, P = 0.031) and prolonged PICU stay (70%, P = 0.045). Fatalities before discharge were recorded in 23.5% of the patients. The most frequent risk factors for viral infections were an age of <12 months old (47.1%), assisted ventilation/intubation (52.9%) and a prolonged PICU stay (55.9%).

CONCLUSION

The results of this study found that CMV was the most common viral infection among infants and children admitted to the PICU in SQUH. CMV was also the leading cause of mortality.

Respiratory syncytial virus genotypes circulating in urban Ghana: February to November 2006

Introduction

Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infection (ALRI) in young children. RSV strains have been divided into 2 major antigenic groups (A and B), which are further divided into several genotypes, but very little is known about its circulating genotypes in Ghana. This study characterized RSV genotypes detected in children with ALRI in Accra between February and November 2006.

Methods

Nasopharyngeal aspirates (NPA) were obtained from children diagnosed with ALRI between February and November 2006. The NPA were screened for RSV using a nested multiplex reverse transcriptase polymerase chain reaction (RT-PCR) method for genotyping RSV. Viral RNA was extracted from the NPA using guanidinium isothiocyanate method and purified with an RNAID commercial kit. Care-givers gave their consent prior to specimen collection. Administered questionnaires captured information on patient demographic and clinical history.

Results

A total of 53 children were enrolled in the study with a male to female ratio of 3:1. Of the 53 NPA analyzed, 60.4% (32/53) were positive for RSV. Subsequent genotypic analysis showed that 72% (23/32) of the 60.4% RSV infections were RSV B only and 28% (9/32) were co-infections of both RSV A and B. Children between the ages of 2 - 12 months were the most affected age group per an RSV infection rate of 37.5% (12/32). No significant difference was detected in the recovery rate of ALRI (98.1%) and RSV (96.9%) positive patients from the infection. One patient died resulting in a mortality rate of 3.1%. Bronchopneumonia (20 out of 32 cases) was the major diagnosis on admission. RSV infection was seasonal dependent, described by 2 peaks in October and April-May.

Conclusion

Both RSV A and RSV B genotypes co-circulated during the study period with RSV B predominating. RSV may possibly be the main pathogen of lower respiratory tract illness during epidemics in the wet seasons. Genotyping by the multiplex RT-PCR is one of the first attempts at molecular diagnosis of RSV infection in Ghana.

Outbreak of adenovirus type 1 severe pneumonia in a French intensive care unit, September-October 2012

We herein describe and analyse the first outbreak of severe pneumonia caused by human adenovirus type1 (HAdV C type 1), which included immunocompetent patients in an intensive care unit (ICU) of Marseille, France, and occurred between September and October 2012. Seven successive patients were diagnosed by HAdV specific real-time polymerase chain reaction with a positive bronchoalveolar lavage. After the collection of nasopharyngeal swabs from healthcare workers, three nurses working night shifts tested positive for HAdV C including one that had exhibited respiratory signs while working one week before the outbreak. She was the most likely source of the outbreak. Our findings suggest that HAdV-1 could be considered as a possible cause of severe pneumonia even in immunocompetent patients with a potential to cause outbreaks in ICUs. HAdV rapid identification and typing is needed to curtail the spread of this pathogen. Reinforcing hand hygiene with antiseptics with demonstrated activity against non-enveloped viruses and ensuring that HCWs with febrile respiratory symptoms avoid direct patient contact are critical measures to prevent transmission of HAdV in healthcare settings.

Can we distinguish pneumonia from wheezy diseases in tachypnoeic children under low-resource conditions? A prospective observational study in four Indian hospitals

BACKGROUND

Acute respiratory infections are the commonest cause of mortality and morbidity in children worldwide. A quarter of all deaths occur in India alone. In order to reduce this disease burden, there is a need for better diagnostic criteria, particularly ones allowing early detection of high-risk children.

METHODS

We enrolled 516 under 5 year olds, in four Indian hospitals, who met WHO age-dependent tachypnoea criteria for pneumonia at presentation. Patients underwent a protocolised examination assessing 29 items, including history, examination, O2 saturation, plus scores for chest X-ray, auscultation and conscious level. Treatment was determined by the emergency room (ER) physician. All children were reviewed at day 4 by a paediatrician and placed into four diagnostic categories: pneumonia, wheezy disease, mixed and non-respiratory.

RESULTS

The majority had wheezy diseases (42.8%). The remainder had pneumonia (35.9%), mixed disease (18.6%) and non-respiratory (2.7%). Best diagnostic predictors for wheezy disease were (auscultation/previous similar episodes) and for pneumonia (auscultation/CXR score). Mortality was 1.6%. Best disease severity predictors were conscious level, weight/age z score and respiratory/pulse rates.

INTERPRETATION

Current tachypnoea-based algorithms significantly overdiagnose pneumonia in children and underdiagnose wheezy diseases. Diagnostic accuracy can be improved by various combinations of clinical variables, but the best single diagnostic predictor is auscultation. Simple criteria can also be defined that reliably detect which tachypnoeic children are at high risk of death or deterioration. Management plans based on these protocols could reduce unnecessary antibiotic use, improve the management of wheezy diseases and reduce mortality by earlier identification of high-risk children.

Epidemiology, etiology, x-ray features, importance of co-infections and clinical features of viral pneumonia in developing countries

Pneumonia is still the number one killer of young children globally, accounting for 18% of mortality in children under 5 years of age. An estimated 120 million new cases of pneumonia occur globally each year. In developing countries, management and prevention efforts against pneumonia have traditionally focused on bacterial pathogens. More recently however, viral pathogens have gained attention as a result of improved diagnostic methods, such as polymerase chain reaction, outbreaks of severe disease caused by emerging pathogens, discovery of new respiratory viruses as well as the decrease in bacterial pneumonia as a consequence of the introduction of highly effective conjugate vaccines. Although the epidemiology, etiology and clinical characterization of viral infections are being studied extensively in the developed world, little data are available from low- and middle-income countries. In this paper, we review the epidemiology, etiology, clinical and radiological features of viral pneumonia in developing countries.

Surveillance for respiratory health care-associated infections among inpatients in 3 Kenyan hospitals, 2010-2012

BACKGROUND

Although health care-associated infections are an important cause of morbidity and mortality worldwide, the epidemiology and etiology of respiratory health care-associated infections (rHAIs) have not been documented in Kenya. In 2010, the Ministry of Health, Kenya Medical Research Institute, and Centers for Disease Control and Prevention initiated surveillance for rHAIs at 3 hospitals.

METHODS

At each hospital, we surveyed intensive care units (ICUs), pediatric wards, and medical wards to identify patients with rHAIs, defined as any hospital-onset (≥3 days after admission) fever (≥38°C) or hypothermia (<35°C) with concurrent signs or symptoms of acute respiratory infection. Nasopharyngeal and oropharyngeal specimens were collected from these patients and tested by real-time reverse transcription polymerase chain reaction for influenza and 7 other viruses.

RESULTS

From April 2010-September 2012, of the 379 rHAI cases, 60.7% were men and 57.3% were children <18 years old. The overall incidence of rHAIs was 9.2 per 10,000 patient days, with the highest incidence in the ICUs. Of all specimens analyzed, 45.7% had at least 1 respiratory virus detected; 92.2% of all positive viral specimens were identified in patients <18 years old.

CONCLUSION

We identified rHAIs in all ward types under surveillance in Kenyan hospitals. Viruses may have a substantial role in these infections, particularly among pediatric populations. Further research is needed to refine case definitions and understand rHAIs in ICUs.

Viral etiology and seasonality of influenza-like illness in Gabon, March 2010 to June 2011

Background

Surveillance of influenza-like illness (ILI) in Central Africa began only recently, and few data are therefore available on the circulation of influenza virus and other respiratory viruses. In Gabon, a Central African country, we established a surveillance network in four major towns in order to analyze cases of ILI among patients who visited health centers between March 2010 and June 2011, and to determine the viral etiology.

Methods

Nasal swabs were sent for analysis to the Centre International de Recherches Médicales de Franceville, where they were screened for 17 respiratory viruses in a multiplex real-time reverse transcription polymerase chain reaction for all pathogens according the following pairs: adenovirus/parainfluenza virus 4, respiratory syncytial virus/human metapneumovirus, parainfluenza virus 1/parainfluenza virus 2, pandemic influenza virus A/seasonal influenza virus A (H1N1, H3N2)/seasonal influenza virus B, human coronaviruses 229E/OC43, human coronaviruses NL63/HKU1, rhinovirus/human parechovirus, and enterovirus/parainfluenza virus 3.

Results

We analyzed a total of 1041 specimens, of which 639 (61%) were positive for at least one virus. Three-quarters of the patients were children under five years old. We therefore focused on this age group, in which 68.1% of patients were positive for at least one virus. The most common viruses were adenoviruses (17.5%), followed by parainfluenza viruses (PIVs) 1–4 (16.8%), enteroviruses (EV) (14.7%), respiratory syncytial virus (RSV) (13.5%), and influenza virus (11.9%). The prevalence of some viruses was subject to geographic and seasonal variations. One-third of positive samples contained more than one virus.

Conclusions

Like most studies in the world, the virus PIVs, EV, RSV, Influenza virus, HRV were predominant among children under five years old in Gabon. An exception is made for adenoviruses which have a high prevalence in our study. However adenoviruses can be detected in asymptomatic persons. These finding gave a better knowledge of the circulation and the seasonality of the viruses involved in ILI in Gabon.

Results from the first six years of national sentinel surveillance for influenza in Kenya, July 2007-June 2013

Background

Recent studies have shown that influenza is associated with significant disease burden in many countries in the tropics, but until recently national surveillance for influenza was not conducted in most countries in Africa.

Methods

In 2007, the Kenyan Ministry of Health with technical support from the CDC-Kenya established a national sentinel surveillance system for influenza. At 11 hospitals, for every hospitalized patient with severe acute respiratory illness (SARI), and for the first three outpatients with influenza-like illness (ILI) per day, we collected both nasopharyngeal and oropharyngeal swabs. Beginning in 2008, we conducted in-hospital follow-up for SARI patients to determine outcome. Specimens were tested by real time RT-PCR for influenza A and B. Influenza A-positive specimens were subtyped for H1, H3, H5, and (beginning in May 2009) A(H1N1)pdm09.

Results

From July 1, 2007 through June 30, 2013, we collected specimens from 24,762 SARI and 14,013 ILI patients. For SARI and ILI case-patients, the median ages were 12 months and 16 months, respectively, and 44% and 47% were female. In all, 2,378 (9.6%) SARI cases and 2,041 (14.6%) ILI cases were positive for influenza viruses. Most influenza-associated SARI cases (58.6%) were in children <2 years old. Of all influenza-positive specimens, 78% were influenza A, 21% were influenza B, and 1% were influenza A/B coinfections. Influenza circulated in every month. In four of the six years influenza activity peaked during July–November. Of 9,419 SARI patients, 2.7% died; the median length of hospitalization was 4 days.

Conclusions

During six years of surveillance in Kenya, influenza was associated with nearly 10 percent of hospitalized SARI cases and one-sixth of outpatient ILI cases. Most influenza-associated SARI and ILI cases were in children <2 years old; interventions to reduce the burden of influenza, such as vaccine, could consider young children as a priority group.

Viral etiologies of hospitalized acute lower respiratory infection patients in China, 2009-2013

BACKGROUND

Acute lower respiratory infections (ALRIs) are an important cause of acute illnesses and mortality worldwide and in China. However, a large-scale study on the prevalence of viral infections across multiple provinces and seasons has not been previously reported from China. Here, we aimed to identify the viral etiologies associated with ALRIs from 22 Chinese provinces.

METHODS AND FINDINGS

Active surveillance for hospitalized ALRI patients in 108 sentinel hospitals in 24 provinces of China was conducted from January 2009-September 2013. We enrolled hospitalized all-age patients with ALRI, and collected respiratory specimens, blood or serum collected for diagnostic testing for respiratory syncytial virus (RSV), human influenza virus, adenoviruses (ADV), human parainfluenza virus (PIV), human metapneumovirus (hMPV), human coronavirus (hCoV) and human bocavirus (hBoV). We included 28,369 ALRI patients from 81 (of the 108) sentinel hospitals in 22 (of the 24) provinces, and 10,387 (36.6%) were positive for at least one etiology. The most frequently detected virus was RSV (9.9%), followed by influenza (6.6%), PIV (4.8%), ADV (3.4%), hBoV (1.9), hMPV (1.5%) and hCoV (1.4%). Co-detections were found in 7.2% of patients. RSV was the most common etiology (17.0%) in young children aged <2 years. Influenza viruses were the main cause of the ALRIs in adults and elderly. PIV, hBoV, hMPV and ADV infections were more frequent in children, while hCoV infection was distributed evenly in all-age. There were clear seasonal peaks for RSV, influenza, PIV, hBoV and hMPV infections.

CONCLUSIONS

Our findings could serve as robust evidence for public health authorities in drawing up further plans to prevent and control ALRIs associated with viral pathogens. RSV is common in young children and prevention measures could have large public health impact. Influenza was most common in adults and influenza vaccination should be implemented on a wider scale in China.

A household-based study of acute viral respiratory illnesses in Andean children

BACKGROUND

Few community studies have measured the incidence, severity and etiology of acute respiratory illness (ARI) among children living at high-altitude in remote rural settings.

METHODS

We conducted active, household-based ARI surveillance among children aged <3 years in rural highland communities of San Marcos, Cajamarca, Peru from May 2009 through September 2011 (RESPIRA-PERU study). ARI (defined by fever or cough) were considered lower respiratory tract infections if tachypnea, wheezing, grunting, stridor or retractions were present. Nasal swabs collected during ARI episodes were tested for respiratory viruses by real-time, reverse-transcriptase polymerase chain reaction. ARI incidence was calculated using Poisson regression.

RESULTS

During 755.1 child-years of observation among 892 children in 58 communities, 4475 ARI were observed, yielding an adjusted incidence of 6.2 ARI/child-year (95% confidence interval: 5.9-6.5). Families sought medical care for 24% of ARI, 4% were classified as lower respiratory tract infections and 1% led to hospitalization. Of 5 deaths among cohort children, 2 were attributed to ARI. One or more respiratory viruses were detected in 67% of 3957 samples collected. Virus-specific incidence rates per 100 child-years were: rhinovirus, 236; adenovirus, 73; parainfluenza virus, 46; influenza, 37; respiratory syncytial virus, 30 and human metapneumovirus, 17. Respiratory syncytial virus, metapneumovirus and parainfluenza virus 1-3 comprised a disproportionate share of lower respiratory tract infections compared with other etiologies.

CONCLUSIONS

In this high-altitude rural setting with low-population density, ARI in young children were common, frequently severe and associated with a number of different respiratory viruses. Effective strategies for prevention and control of these infections are needed.

Clinical care for severe influenza and other severe illness in resource-limited settings: the need for evidence and guidelines

The 2009 influenza A (H1N1) pandemic highlighted the importance of quality hospital care of the severely ill, yet there is evidence that the impact of the 2009 pandemic was highest in low‐ and middle‐income countries with fewer resources. Recent data indicate that death and suffering from seasonal influenza and severe illness in general are increased in resource‐limited settings. However, there are limited clinical data and guidelines for the management of influenza and other severe illness in these settings. Life‐saving supportive care through syndromic case management is used successfully in high‐resource intensive care units and in global programs such as the Integrated Management of Childhood Illness (IMCI). While there are a variety of challenges to the management of the severely ill in resource‐limited settings, several new international initiatives have begun to develop syndromic management strategies for these environments, including the World Health Organization's Integrated Management of Adult and Adolescent Illness Program. These standardized clinical guidelines emphasize syndromic case management and do not require high‐resource intensive care units. These efforts must be enhanced by quality clinical research to provide missing evidence and to refine recommendations, which must be carefully integrated into existing healthcare systems. Realizing a sustainable, global impact on death and suffering due to severe influenza and other severe illness necessitates an ongoing and concerted international effort to iteratively generate, implement, and evaluate best‐practice management guidelines for use in resource‐limited settings.

Nasopharyngeal microbiota in healthy children and pneumonia patients

Our study is the first to compare the nasopharyngeal microbiota of pediatric pneumonia patients and control children by 454 pyrosequencing. A distinct microbiota was associated with different pneumonia etiologies. Viral pneumonia was associated with a high abundance of the operational taxonomic unit (OTU) corresponding to Moraxella lacunata. Patients with nonviral pneumonia showed high abundances of OTUs of three typical bacterial pathogens, Streptococcus pneumoniae complex, Haemophilus influenzae complex, and Moraxella catarrhalis. Patients classified as having no definitive etiology harbored microbiota particularly enriched in the H. influenzae complex. We did not observe a commensal taxon specifically associated with health. The microbiota of the healthy nasopharynx was more diverse and contained a wider range of less abundant taxa.

Clinical utility of PCR for common viruses in acute respiratory illness

BACKGROUND

Acute respiratory illness (ARI) accounts for a large proportion of all visits to pediatric health facilities. Quantitative real-time polymerase chain reaction (qPCR) analyses allow sensitive detection of viral nucleic acids, but it is not clear to what extent specific viruses contribute to disease because many viruses have been detected in asymptomatic children. Better understanding of how to interpret viral findings is important to reduce unnecessary use of antibiotics.

OBJECTIVE

To compare viral qPCR findings from children with ARI versus asymptomatic control subjects.

METHODS

Nasopharyngeal aspirates were collected from children aged ≤5 years with ARI and from individually matched, asymptomatic, population-based control subjects during a noninfluenza season. Samples were analyzed by using qPCR for 16 viruses.

RESULTS

Respiratory viruses were detected in 72.3% of the case patients (n = 151) and 35.4% of the control subjects (n = 74) (P = .001). Rhinovirus was the most common finding in both case patients and control subjects (47.9% and 21.5%, respectively), with a population-attributable proportion of 0.39 (95% confidence interval: 0.01 to 0.62). Metapneumovirus, parainfluenza viruses, and respiratory syncytial virus were highly overrepresented in case patients. Bocavirus was associated with ARI even after adjustment for coinfections with other viruses and was associated with severe disease. Enterovirus and coronavirus were equally common in case patients and control subjects.

CONCLUSIONS

qPCR detection of respiratory syncytial virus, metapneumovirus, or parainfluenza viruses in children with ARI is likely to be causative of disease; detection of several other respiratory viruses must be interpreted with caution due to high detection rates in asymptomatic children.

Beyond malaria--causes of fever in outpatient Tanzanian children

BACKGROUND

As the incidence of malaria diminishes, a better understanding of nonmalarial fever is important for effective management of illness in children. In this study, we explored the spectrum of causes of fever in African children.

METHODS

We recruited children younger than 10 years of age with a temperature of 38°C or higher at two outpatient clinics--one rural and one urban--in Tanzania. Medical histories were obtained and clinical examinations conducted by means of systematic procedures. Blood and nasopharyngeal specimens were collected to perform rapid diagnostic tests, serologic tests, culture, and molecular tests for potential pathogens causing acute fever. Final diagnoses were determined with the use of algorithms and a set of prespecified criteria.

RESULTS

Analyses of data derived from clinical presentation and from 25,743 laboratory investigations yielded 1232 diagnoses. Of 1005 children (22.6% of whom had multiple diagnoses), 62.2% had an acute respiratory infection; 5.0% of these infections were radiologically confirmed pneumonia. A systemic bacterial, viral, or parasitic infection other than malaria or typhoid fever was found in 13.3% of children, nasopharyngeal viral infection (without respiratory symptoms or signs) in 11.9%, malaria in 10.5%, gastroenteritis in 10.3%, urinary tract infection in 5.9%, typhoid fever in 3.7%, skin or mucosal infection in 1.5%, and meningitis in 0.2%. The cause of fever was undetermined in 3.2% of the children. A total of 70.5% of the children had viral disease, 22.0% had bacterial disease, and 10.9% had parasitic disease.

CONCLUSIONS

These results provide a description of the numerous causes of fever in African children in two representative settings. Evidence of a viral process was found more commonly than evidence of a bacterial or parasitic process. (Funded by the Swiss National Science Foundation and others.).

Clinical epidemiology of bocavirus, rhinovirus, two polyomaviruses and four coronaviruses in HIV-infected and HIV-uninfected South African children

Background

Advances in molecular diagnostics have implicated newly-discovered respiratory viruses in the pathogenesis of pneumonia. We aimed to determine the prevalence and clinical characteristics of human bocavirus (hBoV), human rhinovirus (hRV), polyomavirus-WU (WUPyV) and –KI (KIPyV) and human coronaviruses (CoV)-OC43, -NL63, -HKU1 and -229E among children hospitalized with lower respiratory tract infections (LRTI).

Methods

Multiplex real-time reverse-transcriptase polymerase chain reaction was undertaken on archived nasopharyngeal aspirates from HIV-infected and –uninfected children (<2 years age) hospitalized for LRTI, who had been previously investigated for respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus and influenza A/B.

Results

At least one of these viruses were identified in 274 (53.0%) of 517 and in 509 (54.0%) of 943 LRTI-episodes in HIV-infected and -uninfected children, respectively. Human rhinovirus was the most prevalent in HIV-infected (31.7%) and –uninfected children (32.0%), followed by CoV-OC43 (12.2%) and hBoV (9.5%) in HIV-infected; and by hBoV (13.3%) and WUPyV (11.9%) in HIV-uninfected children. Polyomavirus-KI (8.9% vs. 4.8%; p = 0.002) and CoV-OC43 (12.2% vs. 3.6%; p<0.001) were more prevalent in HIV-infected than –uninfected children. Combined with previously-tested viruses, respiratory viruses were identified in 60.9% of HIV-infected and 78.3% of HIV-uninfected children. The newly tested viruses were detected at high frequency in association with other respiratory viruses, including previously-investigated viruses (22.8% in HIV-infected and 28.5% in HIV–uninfected children).

Conclusions

We established that combined with previously-investigated viruses, at least one respiratory virus was identified in the majority of HIV-infected and HIV-uninfected children hospitalized for LRTI. The high frequency of viral co-infections illustrates the complexities in attributing causality to specific viruses in the aetiology of LRTI and may indicate a synergetic role of viral co-infections in the pathogenesis of childhood LRTI.

Human rhinovirus and disease severity in children

OBJECTIVE

To evaluate retrospectively human rhinovirus (HRV) infections in children up to 5 years old and factors involved in disease severity.

METHODS

Nasopharyngeal aspirates from 434 children presenting a broad range of respiratory infection symptoms and severity degrees were tested for presence of HRV and 8 other respiratory viruses. Presence of host risk factors was also assessed.

RESULTS

HRV was detected in 181 (41.7%) samples, in 107 of them as the only agent and in 74 as coinfections, mostly with respiratory syncytial virus (RSV; 43.2%). Moderate to severe symptoms were observed in 28.9% (31/107) single infections and in 51.3% (38/74) coinfections (P = .004). Multivariate analyses showed association of coinfections with lower respiratory tract symptoms and some parameters of disease severity, such as hospitalization. In coinfections, RSV was the most important virus associated with severe disease. Prematurity, cardiomyopathies, and noninfectious respiratory diseases were comorbidities that also were associated with disease severity (P = .007).

CONCLUSIONS

Our study showed that HRV was a common pathogen of respiratory disease in children and was also involved in severe cases, causing symptoms of the lower respiratory tract. Severe disease in HRV infections were caused mainly by presence of RSV in coinfections, prematurity, congenital heart disease, and noninfectious respiratory disease.

Surveillance for hospitalized acute respiratory infection in Guatemala

Acute respiratory infections (ARI) are an important cause of illness and death worldwide, yet data on the etiology of ARI and the population-level burden in developing countries are limited. Surveillance for ARI was conducted at two hospitals in Guatemala. Patients admitted with at least one sign of acute infection and one sign or symptom of respiratory illness met the criteria for a case of hospitalized ARI. Nasopharyngeal/oropharyngeal swabs were collected and tested by polymerase chain reaction for adenovirus, parainfluenza virus types 1,2 and 3, respiratory syncytial virus, influenza A and B viruses, human metapneumovirus, Chlamydia pneumioniae, and Mycoplasma pneumoniae. Urine specimens were tested for Streptococcus pneumoniae antigen. Blood culture and chest radiograph were done at the discretion of the treating physician. Between November 2007 and December 2011, 3,964 case-patients were enrolled. While cases occurred among all age groups, 2,396 (60.4%) cases occurred in children <5 years old and 463 (11.7%) among adults ≥65 years old. Viruses were found in 52.6% of all case-patients and 71.8% of those aged <1 year old; the most frequently detected was respiratory syncytial virus, affecting 26.4% of case-patients. Urine antigen testing for Streptococcus pneumoniae performed for case-patients ≥15 years old was positive in 15.1% of those tested. Among 2,364 (59.6%) of case-patients with a radiograph, 907 (40.0%) had findings suggestive of bacterial pneumonia. Overall, 230 (5.9%) case-patients died during the hospitalization. Using population denominators, the observed hospitalized ARI incidence was 128 cases per 100,000, with the highest rates seen among children <1 year old (1,703 per 100,000), followed by adults ≥65 years old (292 per 100,000). These data, which demonstrate a substantial burden of hospitalized ARI in Guatemala due to a variety of pathogens, can help guide public health policies aimed at reducing the burden of illness and death due to respiratory infections.

Asthma and pneumonia among children less than five years with acute respiratory symptoms in Mulago Hospital, Uganda: evidence of under-diagnosis of asthma

Background

Pneumonia is considered the major cause of mortality among children with acute respiratory disease in low-income countries but may be over-diagnosed at the cost of under-diagnosing asthma. We report the magnitude of asthma and pneumonia among “under-fives” with cough and difficulty breathing, based on stringent clinical criteria. We also describe the treatment for children with acute respiratory symptoms in Mulago Hospital.

Methods

We enrolled 614 children aged 2–59 months with cough and difficulty breathing. Interviews, physical examination, blood and radiological investigations were done. We defined asthma according to Global Initiative for Asthma guidelines. Pneumonia was defined according to World Health Organization guidelines, which were modified by including fever and white cell count, C-reactive protein, blood culture and chest x-ray. Children with asthma or bronchiolitis were collectively referred to as “asthma syndrome” due to challenges of differentiating the two conditions in young children. Three pediatricians reviewed each participant’s case report post hoc and made a diagnosis according to the study criteria.

Results

Of the 614 children, 41.2% (95% CI: 37.3–45.2) had asthma syndrome, 27.2% (95% CI: 23.7–30.9) had bacterial pneumonia, 26.5% (95% CI: 23.1–30.2) had viral pneumonia, while 5.1% (95% CI: 3.5–7.1) had other diagnoses including tuberculosis. Only 9.5% of the children with asthma syndrome had been previously diagnosed as asthma. Of the 253 children with asthma syndrome, 95.3% (95% CI: 91.9–97.5) had a prescription for antibiotics, 87.7% (95% CI: 83.1–91.5) for bronchodilators and 43.1% (95% CI: 36.9–49.4) for steroids.

Conclusion

Although reports indicate that acute respiratory symptoms in children are predominantly due to pneumonia, asthma syndrome contributes a significant proportion. Antibiotics are used irrationally due to misdiagnosis of asthma as pneumonia. There is need for better diagnostic tools for childhood asthma and pneumonia in Uganda.

Prevalence of herpes and respiratory viruses in induced sputum among hospitalized children with non typical bacterial community-acquired pneumonia

Objective

Few comprehensive studies have searched for viruses in infants and young children with community-acquired pneumonia (CAP) in China. The aim of this study was to investigate the roles of human herpes viruses (HHVs) and other respiratory viruses in CAP not caused by typical bacterial infection and to determine their prevalence and clinical significance.

Methods

Induced sputum (IS) samples were collected from 354 hospitalised patients (infants, n = 205; children, n = 149) with respiratory illness (CAP or non-CAP) admitted to Wenling Hospital of China. We tested for HHVs and respiratory viruses using PCR-based assays. The epidemiological profiles were also analysed.

Results

High rate of virus detection (more than 98%) and co-infection (more than 80%) were found among IS samples from 354 hospitalised infants and children with respiratory illness in this study. Of 273 CAP samples tested, CMV (91.6%), HHV-6 (50.9%), RSV (37.4%), EBV (35.5%), HBoV (28.2%), HHV-7 (18.3%) and rhinovirus (17.2%) were the most commonly detected viruses. Of 81 non- CAP samples tested, CMV (63%), RSV (49.4%), HHV-6 (42%), EBV (24.7%), HHV-7 (13.6%) and HBoV (8.6%) were the dominant viruses detected. The prevalence of several viral agents (rhinovirus, bocavirus, adenovirus and CMV) among IS samples of CAP were significantly higher than that of non-CAP control group. We also found the prevalence of RSV coinfection with HHVs was also higher among CAP group than that of non-CAP control.

Conclusions

With sensitive molecular detection techniques and IS samples, high rates of viral identification were achieved in infants and young children with respiratory illness in a rural area of China. The clinical significance of rhinovirus, bocavirus, adenovirus and HHV (especially CMV) infections should receive greater attention in future treatment and prevention studies of CAP in infants and children.

Breastfeeding is associated with decreased pneumonia incidence among HIV-exposed, uninfected Kenyan infants

OBJECTIVE

HIV-exposed uninfected (HEU) infants have higher infectious disease morbidity and mortality than unexposed infants. We determined the incidence and risk factors for pneumonia, a leading cause of infant mortality worldwide, in a cohort of HEU infants. Identifying predictors of pneumonia among HEU infants may enable early identification of those at highest risk.

DESIGN

A retrospective cohort of HEU infants participating in a Kenyan perinatal HIV study, enrolled between 1999 and 2002.

METHODS

Infants were followed monthly from birth to 12 months. Incidence of pneumonia diagnosed at monthly study visits, sick-child visits or by means of averbal autopsy was estimated with a 14-day window for new episodes. Cox proportional hazards regression was used to identify predictors of first pneumonia occurrence.

RESULTS

Among 388 HEU infants with 328 person-years of follow-up, the incidence of pneumonia was 900/1000 child-years [95% confidence interval (CI) 800-1000]. Maternal HIV viral load at 32 weeks' gestation [hazard ratio 1.2 (1.0-1.5) per log10 difference] and being underweight (weight-for-age Z-score <-2) at the previous visit [hazard ratio 1.8 (1.1-2.8)] were associated with increased risk of pneumonia. Breastfed infants had a 47% lower risk of pneumonia than those never breastfed [hazard ratio 0.53 (0.39-0.73)], independent of infant growth, maternal viral load and maternal CD4%. Breastfeeding was also associated with a 74% lower risk of pneumonia-related hospitalization [hazard ratio 0.26 (0.13-0.53)].

CONCLUSIONS

The incidence of pneumonia in this cohort of HEU infants was high. Our observations suggest that maternal viral suppression and breastfeeding may reduce the burden of pneumonia among HEU infants.

Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection

BACKGROUND

Respiratory syncytial virus (RSV) is the leading cause of viral lower respiratory tract infection (LRTI) and hospitalization in infants. Mostly because of the incomplete understanding of the disease pathogenesis, there is no licensed vaccine, and treatment remains symptomatic. We analyzed whole blood transcriptional profiles to characterize the global host immune response to acute RSV LRTI in infants, to characterize its specificity compared with influenza and human rhinovirus (HRV) LRTI, and to identify biomarkers that can objectively assess RSV disease severity.

METHODS AND FINDINGS

This was a prospective observational study over six respiratory seasons including a cohort of infants hospitalized with RSV (n = 135), HRV (n = 30), and influenza (n = 16) LRTI, and healthy age- and sex-matched controls (n = 39). A specific RSV transcriptional profile was identified in whole blood (training cohort, n = 45 infants; Dallas, Texas, US) and validated in three different cohorts (test cohort, n = 46, Dallas, Texas, US; validation cohort A, n = 16, Turku, Finland; validation cohort B, n = 28, Columbus, Ohio, US) with high sensitivity (94% [95% CI 87%-98%]) and specificity (98% [95% CI 88%-99%]). It classified infants with RSV LRTI versus HRV or influenza LRTI with 95% accuracy. The immune dysregulation induced by RSV (overexpression of neutrophil, inflammation, and interferon genes, and suppression of T and B cell genes) persisted beyond the acute disease, and immune dysregulation was greatly impaired in younger infants (<6 mo). We identified a genomic score that significantly correlated with outcomes of care including a clinical disease severity score and, more importantly, length of hospitalization and duration of supplemental O2.

CONCLUSIONS

Blood RNA profiles of infants with RSV LRTI allow specific diagnosis, better understanding of disease pathogenesis, and assessment of disease severity. This study opens new avenues for biomarker discovery and identification of potential therapeutic or preventive targets, and demonstrates that large microarray datasets can be translated into a biologically meaningful context and applied to the clinical setting. Please see later in the article for the Editors' Summary.

Temporal characteristics of respiratory syncytial virus infection in children and its correlation with climatic factors at a public pediatric hospital in Suzhou

BACKGROUND

Respiratory syncytial virus (RSV) is the most important viral pathogen in infants and children. It is important to analyze RSV epidemic patterns and related relevant factors in order to prevent further infections and related complications.

OBJECTIVE

To explore the relationship between RSV infection rate in hospitalized children from Suzhou area and climatic factors.

STUDY DESIGN

42,664 nasopharyngeal specimens from hospitalized children with acute respiratory infections were screened for RSV antigens using direct immunofluorescence. 472 RSV positive samples were randomly selected and performed real-time PCR to identify RSV subtype. Monthly meteorological data in Suzhou area was collected (average temperature, relative humidity, precipitation, total sunshine, and average wind speed) from 2001 to 2011. The relation between RSV infections and climatic factors was evaluated using correlation and stepwise regression analyses.

RESULTS

The annual RSV infection rate in hospitalized children in Suzhou from 2001 to 2011 varied between 11.85% and 27.30%. The highest monthly infection rates occurred from November to April. The time interval from November to April was considered the infection season. Seasonal RSV infection rates from 2001 to 2010 were 40.75%, 22.72%, 39.93%, 27.37%, 42.71%, 21.28%, 38.57%, 19.86%, and 29.73%. The infection rate of any season was statistically different from the next season. There was no significant difference in RSV infection rates in the 2010-2011 and 2009-2010 epidemic seasons. Among the 472 randomly selected RSV positive samples, 412 were found to be RSV subtype A (RSV-A), while 60 subtype B (RSV-B). The monthly RSV infection rate was negatively correlated with monthly average temperature (r=-0.84), total sunshine (r=-0.47), precipitation (r=-0.31), relative humidity (r=-0.20), and average wind speed (r=-0.20), (P<0.05). Stepwise regression analysis showed monthly average temperature fit into a linear model (R(2)=0.64, P<0.01) with a regression coefficient of -1.52 (t=15.21, P<0.01).

CONCLUSIONS

RSV infection in Suzhou occurred most frequently between November and April. The number of infections peaked every other year. Abnormally high infection rate in non-epidemic season only caused by RSV-A. Ambient temperature played an important role in the development of RSV infection.

Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border

Background

Pneumonia is a significant cause of morbidity and mortality in the developing world. Viruses contribute significantly to pneumonia burden, although data for low-income and tropical countries are scarce. The aim of this laboratory-enhanced, hospital-based surveillance was to characterise the epidemiology of respiratory virus infections among refugees living on the Thailand-Myanmar border.

Methods

Maela camp provides shelter for ~45,000 refugees. Inside the camp, a humanitarian organisation provides free hospital care in a 158-bed inpatient department (IPD). Between 1st April 2009 and 30th September 2011, all patients admitted to the IPD with a clinical diagnosis of pneumonia were invited to participate. Clinical symptoms and signs were recorded and a nasopharyngeal aspirate (NPA) collected. NPAs were tested for adenoviruses, human metapneumovirus (hMPV), influenza A & B, and RSV by PCR.

Results

Seven hundred eight patient episodes (698 patients) diagnosed as pneumonia during the enhanced surveillance period were included in this analysis. The median patient age was 1 year (range: < 1-70), and 90.4% were aged < 5 years. At least one virus was detected in 53.7% (380/708) of episodes. Virus detection was more common in children aged < 5 years old (<1 year: OR 2.0, 95% CI 1.2-3.4, p = 0.01; 1-4 years: OR 1.4, 95% CI 0.8-2.3, p = 0.2). RSV was detected in 176/708 (24.9%); an adenovirus in 133/708 (18.8%); an influenza virus in 68/708 (9.6%); and hMPV in 33/708 (4.7%). Twenty-eight episodes of multiple viral infections were identified, most commonly adenovirus plus another virus. RSV was more likely to be detected in children <5 years (OR 12.3, 95% CI 3.0-50.8, p = 0.001) and influenza viruses in patients ≥5 years (OR 2.8, 95% CI 1.5-5.4, p = 0.002). IPD treatment was documented in 702/708 cases; all but one patient received antimicrobials, most commonly a beta-lactam (amoxicillin/ampicillin +/−gentamicin in 664/701, 94.7%).

Conclusions

Viral nucleic acid was identified in the nasopharynx in half the patients admitted with clinically diagnosed pneumonia. Development of immunisations targeting common respiratory viruses is likely to reduce the incidence of pneumonia in children living refugee camps and similar settings.

Factors associated with asthma among under-fives in Mulago hospital, Kampala Uganda: a cross sectional study

BACKGROUND

Asthma is the most common chronic childhood illness, with rapidly increasing prevalence in low-income countries. Among young children, asthma is often under-diagnosed.We investigated the factors associated with asthma among under-fives presenting with acute respiratory symptoms at Mulago hospital, Uganda.

METHODS

A hospital-based cross sectional study of 614 children with cough and/or difficult breathing, and fast breathing, was conducted between August 2011 and June 2012. A questionnaire focusing on clinical history of the child was administered to the caretakers. A physical examination and, laboratory and radiological investigations were done. Asthma was defined according to GINA (Global Initiative for Asthma) guidelines which were modified by excluding the symptom of "chest tightness", spirometry/peak expiratory flow measurements and by adding chest x-ray findings to distinguish asthma from pneumonia. A panel of three paediatricians reviewed the participants' case reports and, guided by the study definitions, made a diagnosis of asthma or other. Multivariable logistic regression analysis was done to determine factors independently associated with asthma.

RESULTS

Of the 614 children, 128 (20.8%) had asthma, 125 (20.4%) bronchiolitis, 167 (27.2%) bacterial pneumonia only, 163 (26.5%) viral pneumonia while 31 (5.1%) had other diagnoses including pulmonary tuberculosis. The majority (71.1%) of children with asthma were aged ≥ 12 months. Factors associated with asthma included maternal asthma (AOR 2.4, 95% CI 1.2, 4.6), a history of allergy in the patient (AOR 2.6, 95% CI 1.2, 5.4,), use of gas for cooking (AOR 3.8, 95% CI 1.2, 13.3), prematurity (AOR 9.3, 95% CI 1.2, 83.3) and high level of education of caretaker (AOR 9.1, 95% CI 1.1, 72.8).

CONCLUSION

Maternal asthma, a history of allergy in the patient, use of gas for cooking, prematurity and high level of education of caretaker were significantly associated with asthma. There is need for studies to explore the role of the above factors in development and exacerbation of childhood asthma to provide information that can be used to design strategies for asthma prevention and control.

Association of the CT values of real-time PCR of viral upper respiratory tract infection with clinical severity, Kenya

Quantitative real-time polymerase chain reaction (qRT-PCR) assay of the upper respiratory tract is used increasingly to diagnose lower respiratory tract infections. The cycle threshold (CT ) values of qRT-PCR are continuous, semi-quantitative measurements of viral load, although interpretation of diagnostic qRT-PCR results are often categorized as positive, indeterminate, or negative, obscuring potentially useful clinical interpretation of CT values. From 2008 to 2010, naso/oropharyngeal swabs were collected from outpatients with influenza-like illness, inpatients with severe respiratory illness, and asymptomatic controls in rural Kenya. CT values of positive specimens (i.e., CT values < 40.0) were compared by clinical severity category for five viruses using Mann-Whitney U-test and logistic regression. Among children <5 years old we tested with respiratory syncytial virus (RSV), inpatients had lower median CT values (27.2) than controls (35.8, P = 0.008) and outpatients (34.7, P < 0.001). Among children and older patients infected with influenza virus, outpatients had the lowest median CT values (29.8 and 24.1, respectively) compared with controls (P = 0.193 for children, P < 0.001 for older participants) and inpatients (P = 0.009 for children, P < 0.001 for older participants). All differences remained significant in logistic regression when controlling for age, days since onset, and coinfection. CT values were similar for adenovirus, human metapneumovirus, and parainfluenza virus in all severity groups. In conclusion, the CT values from the qRT-PCR of upper respiratory tract specimens were associated with clinical severity for some respiratory viruses.

Viral etiology and clinical profiles of children with severe acute respiratory infections in China

Background

No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute respiratory infection (SARI) in China during 2009 H1N1 pandemic and post-pandemic period.

Methods

Cohort of 370 hospitalized children (1 to 72 months) with SARI from May 2008 to March 2010 was enrolled in this study. Nasopharyngeal aspirate (NPA) specimens were tested by a commercial assay for 18 respiratory viral targets. The viral distribution and its association with clinical character were statistically analyzed.

Results

Viral pathogen was detected in 350 (94.29%) of children with SARI. Overall, the most popular viruses were: enterovirus/rhinovirus (EV/RV) (54.05%), respiratory syncytial virus (RSV) (51.08%), human bocavirus (BoCA) (33.78%), human parainfluenzaviruse type 3 (PIV3) (15.41%), and adenovirus (ADV) (12.97%). Pandemic H1N1 was the dominant influenza virus (IFV) but was only detected in 20 (5.41%) of children. Moreover, detection rate of RSV and human metapneumovirus (hMPV) among suburb participants were significantly higher than that of urban area (P<0.05). Incidence of VSARI among suburb participants was also significant higher, especially among those of 24 to 59 months group (P<0.05).

Conclusion

Piconaviruses (EV/RV) and paramyxoviruses are the most popular viral pathogens among children with SARI in this study. RSV and hMPV significantly increase the risk of SARI, especially in children younger than 24 months. Higher incidence of VSARI and more susceptibilities to RSV and hMPV infections were found in suburban patients.

Clinical characteristics and outcomes of influenza and other influenza-like illnesses in Mexico City

BACKGROUND

Influenza-like illnesses (ILI) are estimated to cause millions of deaths annually. Despite this disease burden, the etiologic causes of ILI are poorly described for many geographical regions.

METHODS

Beginning in April 2010, we conducted an observational cohort study at five hospitals in Mexico City, enrolling subjects who met the criteria for ILI. Evaluations were conducted at enrollment and on day 28, with the collection of clinical data and a nasopharyngeal swab (or nasal aspirate in children). Swabs were tested by multiplex PCR for 15 viral pathogens and real-time PCR for influenza.

RESULTS

During the first year, 1065 subjects were enrolled in this study, 55% of whom were hospitalized; 24% of all subjects were children. One or more pathogens were detected by PCR in 64% of subjects, most commonly rhinovirus (25% of all isolates) and influenza (24% of isolates). Six percent of subjects died, and of those, 54% had no pathogen identified. Rhinovirus was the most common pathogen among those who died, although it did not have the highest case fatality rate.

CONCLUSIONS

Multiple respiratory viruses beyond influenza are associated with significant morbidity and mortality among adults and children in Mexico City. Detection of these agents could be useful for the adjustment of antibiotic treatment in severe cases.

The viral aetiology of influenza-like illnesses in Kampala and Entebbe, Uganda, 2008

BACKGROUND

As the threat of zoonoses and the emergence of pandemic-prone respiratory viruses increases, there is a need to establish baseline information on the incidence of endemic pathogens in countries worldwide.

OBJECTIVES

To investigate the presence of viruses associated with influenza-like illnesses (ILI) in Uganda.

METHODS

A cross-sectional study was conducted in which nasopharyngeal swab specimens were collected from patients diagnosed with ILI in Kampala and Entebbe between 14 August 2008 - 15 December 2008. A multiplex polymerase chain reaction assay for detecting 12 respiratory viruses was used.

RESULTS

A total of 369 patients (52.3% females) was enrolled; the median age was 6 years (range 1-70). One or more respiratory viruses were detected in 172 (46.6%) cases and their prevalence were influenza A virus (19.2%), adenovirus (8.7%), human rhinovirus A (7.9%), coronavirus OC43 (4.3%), parainfluenza virus 1 (2.7%), parainfluenza virus 3 (2.7%), influenza B virus (2.2%), respiratory syncytial virus B (2.2%), human metapneumovirus (1.4%), respiratory syncytial virus A (1.1%), parainfluenza virus 2 (0.5%) and coronavirus 229E (0.5%). There were 24 (14.0%) mixed infections.

CONCLUSIONS

This study identified some of the respiratory viruses associated with ILI in Uganda. The circulation of some of the viruses was previously unknown in the study population. These results are useful in order to guide future surveillance and case management strategies involving respiratory illnesses in Uganda.

The impact of viral infections in children with community-acquired pneumonia

For many years viral causes of community-acquired pneumonia were often been given limited attention. The number of published studies on influenza alone increased fivefold from 2001 to 2010. Specifically several studies have underlined that the involvement of viruses in community-acquired pneumonia has been underestimated, and this underestimation has been attributed to a lack of appropriate diagnostic methods. Now, with the advent of modern molecular assays, it is well recognized that viruses account for the largest proportion of community-acquired pneumonia in preschool children in both developed and developing countries. Respiratory syncytial virus, influenza virus, adenovirus, and parainfluenza virus are the major pathogens involved, but the relative importance of additional viruses (rhinoviruses, bocavirus, human metapneumovirus) is increasing and will be better defined by future research.

Viral etiology of acute respiratory infection in Gansu Province, China, 2011

Background

Acute respiratory infections (ARIs) are the leading cause of children and their leading killer. ARIs are responsible for at least six percent of the world's disability and death. Viruses are one of the most common agents causing ARIs. Few studies on the viral etiology and clinical characteristics of ARIs have been performed in the northwest region of China, including Gansu Province.

Methods

Clinical and demographic information and throat swabs were collected from 279 patients from January 1st to December 30st, 2011. Multiplex RT-PCR was performed to detect 16 respiratory viral pathogens.

Results

279 patients were admitted for ARIs. The patients aged from 1 month to 12 years, with the median age of 2 years. Of which, 105 (37.6%) were positive for at least one pathogen. A total of 136 respiratory viral pathogens were identified from the 105 patients. Respiratory syncytial virus (RSV) was the most frequently detected pathogen (26.5%, 36/136), followed by parainfluenza virus (PIV) 1–3 (22.1%, 30/136), human rhinovirus (HRV) (21.3%, 29/136), human coronavirus (CoV) (10.3%, 14/136) and human adenovirus (HAdV) (9.6%, 13/136). Influenza A (Flu A), human metapneumovirus (hMPV) and human bocavirus (BoCA) were found 4.4%, 3.7% and 2.2%, respectively. Influenza B (Flu B) and seasonal influenza A H1N1(sH1N1) were not detected. Single-infections were detected in 30.5% (85/279) of cases. RSV was the most common pathogens in patients under 1 year and showed seasonal variation with peaks during winter and spring.

Conclusions

This paper presents data on the epidemiology of viral pathogens associated with ARIs among children in Gansu Province, China. RSV is most frequently detected in our study. The findings could serve as a reference for local CDC in drawing up further plans to prevent and control ARIs.

Afriflu2--second international workshop on influenza vaccination in the African continent--8 November 2012, Cape Town (South Africa)

The second meeting of the Afriflu conferences took place in Cape Town, South Africa, with over 60 participants from 15 countries in Africa and also outside the continent. Significant progress in surveillance has been made in better understanding the illness burden of influenza on the continent, which limited evidence suggests is greater than that in the developed world. In southern Africa HIV and TB coinfections play a major role in increasing hospitalisation and mortality, while elsewhere in Africa other cofactors still need to be determined. There is currently no indigenous vaccine production in sub-Saharan Africa and only one facility, based in South Africa, capable of filling imported bulk. Innovative vaccine strategies will need to be explored, such as maternal immunisation, and also the possibility of other influenza vaccine options, such as live attenuated influenza vaccine for young children. Sustained indigenous vaccine production is essential for the continent to have vaccine security in the event of a pandemic even though establishing local production faces considerable challenges especially ensuring adequate markets on the continent. There is an urgent need to develop effective communication messages for decision makers as well as healthcare workers addressing the importance of influenza even in the face of the major competing health burdens of the continent.

First introduction of pandemic influenza A/H1N1 and detection of respiratory viruses in pediatric patients in Central African Republic

Background

Acute viral respiratory illnesses in children in sub-Saharan Africa have received relatively little attention, although they are much more frequent causes of morbidity and mortality than in developed countries. Active surveillance is essential to identify the causative agents and to improve clinical management, especially in the context of possible circulation of pandemic viruses.

Findings

A prospective study was conducted in the Central African Republic (CAR) between January and December 2010 among infants and children aged 0–15 years attending sentinel sites for influenza-like illness or acute respiratory illness. Nasopharyngeal swabs were collected, and one-step real-time and multiplex reverse transcription-polymerase chain reaction were used to detect respiratory viruses. Respiratory viruses were detected in 49 of the 329 (14.9%) nasopharyngeal samples: 29 (8.8%) contained influenza viruses (5 (1.5%) had pandemic influenza A/H1N1 virus and 24 (7.3%) had influenza B viruses), 11 (3.3%) contained parainfluenza viruses types 1 and 3 and 9 (2.7%) contained human respiratory syncytial virus. Most cases were detected during the rainy season in the CAR. Analysis of the amplicon sequences confirmed the identity of each detected virus.

Conclusions

The influenza surveillance system in the CAR has provided valuable data on the seasonality of influenza and the circulation of other respiratory viruses. Our network could therefore play a valuable role in the prevention and control of influenza epidemics in the CAR.

PATH Influenza Vaccine Project: accelerating the development of new influenza vaccines for low-resource countries

The 2009 influenza A/H1N1 pandemic demonstrated that a pandemic influenza virus has the potential to spread more rapidly in today's highly interconnected world than in the past. While pandemic morbidity and mortality are likely to be greatest in low-resource countries, manufacturing capacity and access to influenza vaccines predominantly exist in countries with greater resources and infrastructure. Even with recently expanded manufacturing capacity, the number of doses available within a 6-month timeframe would be inadequate to fully immunize the global population if the decision to implement a global vaccination program were made today. Improved, affordable vaccines are needed to limit the consequences of a global influenza outbreak and protect low-resource populations. PATH's Influenza Vaccine Project is supporting a range of activities in collaboration with private- and public-sector partners to advance the development of promising influenza vaccines that can be accessible and affordable for people in low-resource countries.

Genetic characterization of human respiratory syncytial virus detected in hospitalized children in the Philippines from 2008 to 2012

BACKGROUND

Human respiratory syncytial virus (HRSV) is the leading cause of acute lower respiratory tract infection in infants and young children. However, molecular characteristic of HRSV is still unknown in the Philippines.

OBJECTIVE

To describe the molecular epidemiology of circulating HRSV detected in the Philippines.

STUDY DESIGN

From May 2008 to April 2012, nasopharyngeal swabs were collected from infants and children aged between 7 days and 14 years who were hospitalized with severe pneumonia. HRSV was detected by nested PCR targeting M2 gene, and C-terminus of the G gene was sequenced for phylogenetic analysis.

RESULT

Out of total 2150 samples, 19.3% (n = 415) were positive for HRSV, and 65.0% of them (n = 270) were identified as HRSV-A and 35.0% (n = 145) as HRSV-B. There were two major HRSV outbreaks: between June 2008 and February 2009, and between June and March 2012. Majority of HRSV strains detected during the former outbreak were HRSV-A (97.5%, 203/208) whereas during the later outbreak, both HRSV-A (54/158, 34.2%) and HRSV-B (104/158, 65.8%) were detected. All HRSV-A strains were classified as genotype NA1 and all HRSV-B as genotype BA, which had 60-nucleotide duplication in secondary hypervariable region of the G gene. Among HRSV-B positive samples, there were 2 distinct clusters with unique amino acid changes and low homology in compared to other strains in BA, suggesting emergence of new variant of HRSV-B.

CONCLUSION

The study provides an overview of the genetic variation in circulating HRSV viruses in the Philippines along with identification of possibly a novel variant of HRSV-B.

Epidemiology, seasonality, and burden of influenza and influenza-like illness in urban and rural Kenya, 2007-2010

BACKGROUND

The epidemiology and burden of influenza remain poorly defined in sub-Saharan Africa. Since 2005, the Kenya Medical Research Institute and Centers for Disease Control and Prevention-Kenya have conducted population-based infectious disease surveillance in Kibera, an urban informal settlement in Nairobi, and in Lwak, a rural community in western Kenya.

METHODS

Nasopharyngeal and oropharyngeal swab specimens were obtained from patients who attended the study clinic and had acute lower respiratory tract (LRT) illness. Specimens were tested for influenza virus by real-time reverse-transcription polymerase chain reaction. We adjusted the incidence of influenza-associated acute LRT illness to account for patients with acute LRT illness who attended the clinic but were not sampled.

RESULTS

From March 2007 through February 2010, 4140 cases of acute LRT illness were evaluated in Kibera, and specimens were collected from 1197 (27%); 319 (27%) were positive for influenza virus. In Lwak, there were 6733 cases of acute LRT illness, and specimens were collected from 1641 (24%); 359 (22%) were positive for influenza virus. The crude and adjusted rates of medically attended influenza-associated acute LRT illness were 6.9 and 13.6 cases per 1000 person-years, respectively, in Kibera, and 5.6 and 23.0 cases per 1000 person-years, respectively, in Lwak. In both sites, rates of influenza-associated acute LRT illness were highest among children <2 years old and lowest among adults ≥50 years old.

CONCLUSION

In Kenya, the incidence of influenza-associated acute LRT illness was high in both rural and urban settings, particularly among the most vulnerable age groups.

Respiratory viral coinfections identified by a 10-plex real-time reverse-transcription polymerase chain reaction assay in patients hospitalized with severe acute respiratory illness--South Africa, 2009-2010

BACKGROUND

Data about respiratory coinfections with 2009 pandemic influenza A virus subtype H1N1 during the 2009-2010 influenza pandemic in Africa are limited. We used an existing surveillance program for severe acute respiratory illness to evaluate a new multiplex real-time polymerase chain reaction assay and investigate the role of influenza virus and other respiratory viruses in pneumonia hospitalizations during and after the influenza pandemic in South Africa.

METHODS

The multiplex assay was developed to detect 10 respiratory viruses, including influenza A and B viruses, parainfluenza virus types 1-3, respiratory syncytial virus (RSV), enterovirus, human metapneumovirus (hMPV), adenovirus (AdV), and rhinovirus (RV), followed by influenza virus subtyping. Nasopharyngeal and oropharyngeal specimens were collected from patients hospitalized with pneumonia at 6 hospitals during 2009-2010.

RESULTS

Validation against external quality controls confirmed the high sensitivity (91%) and specificity (100%) and user-friendliness, compared with other PCR technologies. Of 8173 patients, 40% had single-virus infections, 17% had coinfections, and 43% remained negative. The most common viruses were RV (25%), RSV (14%), AdV (13%), and influenza A virus (5%). Influenza virus, RSV, PIV type 3, and hMPV showed seasonal patterns.

CONCLUSION

The data provide a better understanding of the viral etiology of hospitalized cases of pneumonia and demonstrate the usefulness of this multiplex assay in respiratory disease surveillance in South Africa.

Influenza surveillance in Zambia, 2008-2009

BACKGROUND

Limited information exists about influenza viruses in Africa. We used data from a new sentinel surveillance system to investigate the seasonality and characteristics of influenza, including pandemic (pdm) influenza A H1N1, in Zambia.

METHODS

In June 2008, we established sentinel surveillance for influenza-like illness (ILI) and severe acute respiratory illness (SARI) at 4 healthcare facilities in Zambia. Nasopharyngeal and oropharyngeal swabs and structured questionnaires were collected from eligible patients and samples were tested by real-time reverse-transcription polymerase chain reaction for influenza virus types and subtypes.

RESULTS

From June 2008 to December 2009, we collected 1234 specimens, of which 334 (27%) were ILI, and 900 (63%) were SARI. Overall, 4% (57) of specimens were positive for influenza. The influenza detection rate in ILI and SARI cases was 5% (17/334) and 4% (40/900), respectively. Among all influenza cases, 54 (95%) were influenza A and 3 (5%) were influenza B. Of the influenza A viruses, 16 (30%) were A(H1N1)pdm09, 29 (54%) were seasonal A(H1N1), 6 (11%) were A(H3N2), and 4 (7%) were unsubtyped. The detection rate for A(H1N1)pdm09 cases was highest in persons aged 5-24 years (5/98; 5%), 25-44 years (4/78; 5%), and 45-64 years (1/17; 6%). Conversely, for seasonal influenza the detection rate was highest in children aged 1-4 years (18/294; 6%). Influenza virus circulation peaked during June-August in both years and A(H1N1)pdm09 occurred at the end of the influenza season in 2009.

CONCLUSIONS

Seasonal influenza virus infection was found to be associated with both mild and severe respiratory illness in Zambia. Future years of surveillance are necessary to better define the seasonality and epidemiology of influenza in the country.

Challenges of establishing routine influenza sentinel surveillance in Ethiopia, 2008-2010

Ethiopia launched influenza surveillance in November 2008. By October 2010, 176 patients evaluated at 5 sentinel health facilities in Addis Ababa met case definitions for influenza-like illness or severe acute respiratory illness (SARI). Most patients (131 [74%]) were children aged 0-4 years. Twelve patients (7%) were positive for influenza virus. Most patients (109 [93%]) were aged <5 years, of whom only 3 (2.8%) had laboratory-confirmed influenza. Low awareness of influenza by healthcare workers, misperceptions regarding case definitions, and insufficient human resources at sites could have potentially led to many missed cases, resulting in suboptimal surveillance.

Clinic- and hospital-based sentinel influenza surveillance, Uganda 2007-2010

BACKGROUND

To assess the epidemiology and seasonality of influenza in Uganda, we established a sentinel surveillance system for influenza in 5 hospitals and 5 outpatient clinics in 4 geographically distinct regions, using standard case definitions for influenzalike illness (ILI) and severe acute respiratory illness (SARI).

METHODS

Nasopharyngeal and oropharyngeal specimens were collected from April 2007 through September 2010 from patients with ILI and SARI aged ≥ 2 months, tested for influenza A and B with real-time reverse-transcription polymerase chain reaction, and subtyped for seasonal A/H1, A/H3, A/H5, and 2009 pandemic influenza A (pH1N1).

RESULTS

Among the 2758 patients sampled, 2656 (96%) enrolled with ILI and 101 (4%) with SARI. Specimens from 359 (13.0%) were positive for influenza; 267 (74.4%) were influenza A, and 92 (25.6%) were influenza B. The median age of both patients with ILI and patients with SARI was 4 years (range, 2 months to 67 years); patients aged 5-14 years had the highest influenza-positive percentage (19.6%), and patients aged 0-4 years had the lowest percentage (9.1%). Influenza circulated throughout the year, but the percentage of influenza-positive specimens peaked during June-November, coinciding with the second rainy season.

CONCLUSIONS

Continued and increased surveillance is needed to better understand the morbidity and mortality of influenza in Uganda.

Viral etiology of influenza-like illnesses in Cameroon, January-December 2009

Background. No information is available on the viral etiology of upper respiratory tract infections in Cameroon.

Methods. We prospectively enrolled outpatients with influenza-like illness (ILI) presenting at 14 sentinel clinics located across the country from January through December 2009. The specimens were tested using real-time and multiplex reverse-transcription polymerase chain reaction methods for the detection of 15 RNA respiratory viruses.

Results. We detected at least 1 respiratory virus in 365 of 561 specimens (65.1%). Overall, influenza virus was the most commonly detected virus (28.2% of specimens), followed by human rhinovirus (17.8%); parainfluenza virus (PIV) types 1–4 (7.5%); enterovirus (5.9%); respiratory syncytial virus (RSV; 5.7%); human coronavirus (HCoV) OC43, 229E, NL63, and HKU1 (5.3%); and human metapneumovirus (HMPV; 5.0%). RSV (26 of 31 specimens [83.9%]), PIV (30 of 39 [76.9%]), and HRV (64 of 99 [64.6%]) were most common among children <5 years of age. Coinfections were found in 53 of 365 positive specimens (14.5%), and most (71.7%) were in children <5 years of age. While influenza virus, enterovirus, RSV, and HMPV had a defined period of circulation, the other viruses were detected throughout the year.

Conclusions. We found that respiratory viruses play an important role in the etiology of ILI in Cameroon, particularly in children <5 years of age.

Molecular epidemiology and disease severity of human respiratory syncytial virus in Vietnam

Respiratory syncytial virus (RSV) is a major cause of acute respiratory infections (ARIs) in children worldwide and can cause high mortality, especially in developing countries. However, information on the clinical and molecular characteristics of RSV infection in developing countries is limited. From April 2010 to May 2011, 1,082 nasopharyngeal swabs were collected from children with ARI admitted to the Children's Hospital 2, Ho Chi Minh City, Vietnam. Samples were screened for RSV and genotyped by reverse transcription-PCR and sequencing. Demographic and clinical data was also recorded. RSV was found in 23.8% (257/1,082) of samples. RSV A was the dominant subgroup, accounting for 91.4% (235/257), followed by RSV B, 5.1% (13/257), and 9 cases (3.5%) were mixed infection of these subgroups. The phylogenetic analysis revealed that all group A strains belonged to the GA2 genotype. All group B strains belonged to the recently identified BA genotype, and further clustered into 2 recently described subgenotypes BA9 and BA10. One GA2 genotype strain had a premature stop codon which shortened the G protein length. RSV infection was significantly associated with younger age and higher severity score than those without. Co-infection with other viruses did not affect disease severity. RSV A caused more severe disease than RSV B. The results from this study will not only contribute to the growing database on the molecular diversity of RSV circulating worldwide but may be also useful in clinical management and vaccine development.

Viral and bacterial interactions in the upper respiratory tract

Respiratory infectious diseases are mainly caused by viruses or bacteria that often interact with one another. Although their presence is a prerequisite for subsequent infections, viruses and bacteria may be present in the nasopharynx without causing any respiratory symptoms. The upper respiratory tract hosts a vast range of commensals and potential pathogenic bacteria, which form a complex microbial community. This community is assumed to be constantly subject to synergistic and competitive interspecies interactions. Disturbances in the equilibrium, for instance due to the acquisition of new bacteria or viruses, may lead to overgrowth and invasion. A better understanding of the dynamics between commensals and pathogens in the upper respiratory tract may provide better insight into the pathogenesis of respiratory diseases. Here we review the current knowledge regarding specific bacterial–bacterial and viral–bacterial interactions that occur in the upper respiratory niche, and discuss mechanisms by which these interactions might be mediated. Finally, we propose a theoretical model to summarize and illustrate these mechanisms.

High rates of pneumonia in children under two years of age in a South East Asian refugee population

BACKGROUND

There are an estimated 150 million episodes of childhood pneumonia per year, with 11-20 million hospital admissions and 1.575 million deaths. Refugee children are particularly vulnerable, with poorly defined pneumonia epidemiology.

METHODS

We followed a birth cohort of 955 refugee infants, born over a one-year period, until two years of age. Clinical and radiographic pneumonia were diagnosed according to WHO criteria. Detailed characteristics were collected to determine risk factors for clinical, radiological and multiple episodes of pneumonia. Investigations were taken during a pneumonia episode to help determine or to infer an aetiological diagnosis.

FINDINGS

The incidence of clinical pneumonia was 0.73 (95% CI 0.70-0.75) episodes per child year (/CY) and of radiological primary endpoint pneumonia (PEP) was 0.22/CY (95% CI 0.20-0.24). The incidence of pneumonia without severe signs was 0.50/CY (95% CI 0.48-0.53), severe pneumonia 0.15/CY (95% CI 0.13-0.17) and very severe pneumonia 0.06/CY (0.05-0.07). Virus was detected, from a nasopharyngeal aspirate, in 61.3% of episodes. A reduced volume of living space per person (IRR 0.99, 95% CI 0.99-1.0, p = 0.003) and young maternal age (IRR 1.59, 95% CI 1.12-2.27, p = 0.01) were risk factors for developing pneumonia. The risk of a child having >1 episode of pneumonia was increased by having a shorter distance to the next house (IRR 0.86, 95% CI 0.74-1.00, p = 0.04). Infants were at risk of having an episode of PEP if there was a shorter distance from stove to bed (IRR 0.89, 95% CI 0.80-0.99, p = 0.03). Raised CRP and neutrophil values were associated with PEP.

CONCLUSIONS

There was a high incidence of pneumonia in young children in this SE Asian refugee population. Viral infections were important, however CXR and non-specific marker findings suggested that bacteria may be involved in up to a third of cases.

Epidemiology of community-acquired Mycoplasma Pneumoniae respiratory tract infections among hospitalized Chinese children, including relationships with meteorological factors

BACKGROUND

Mycoplasma Pneumoniae (M. pneumoniae) is a common cause of respiratory tract infections (RTIs), especially in children. Combined diagnostic techniques have provided more reliable information about the epidemiology of infections by this pathogen. The relationship between M. pneumoniae RTIs and climatic conditions is not well documented in the literature.

AIMS

To study the epidemiology of M. pneumoniae infections in hospitalized children with RTIs and its association with meteorological factors.

METHODS

Samples were obtained from children with RTIs and tested for M. pneumoniae by PCR and ELISA. Meanwhile, meteorological factors were recorded.

RESULTS

M. pneumoniae was identified in 11.02% of the 8,157 specimens. There were significant differences among the annual distribution of infections (χ(2) =130.13, P<0.0001) and among different seasons (χ(2) =93.59, P<0.0001). Of the total number of patients with M. pneumoniae infections, 14.5% were infected with more than one pathogen. M. pneumoniae infection strongly correlated with mean temperature. Children with a single M. pneumoniae infection had significantly higher neutrophil percentages and CRP levels than children with co-infections.

CONCLUSIONS

M. pneumoniae is one of the most commonly held pathogens, according to the 5-year surveillance. M. pneumoniae infection has its own epidemic season, especially in the summer. Mean temperature is the main meteorological factor affecting the epidemiology of M. pneumoniae infections.

Acute viral lower respiratory tract infections in Cambodian children: clinical and epidemiologic characteristics

BACKGROUND

Viruses are detected in most hospitalized children admitted for acute respiratory infections. Etiologic understanding is needed to improve clinical management and prevention, particularly in resource-limited tropical countries.

METHODS

A 3-year prospective descriptive study was conducted among Cambodian children admitted to 2 provincial hospitals for acute lower respiratory tract infection. Molecular detection for 18 viral pathogens using multiplex polymerase chain reaction/reverse transcription polymerase chain reactions was performed.

RESULTS

We enrolled 1006 children less than 5 years of age of whom 423 (42%), 428 (42%) and 155 (16%) had pneumonia, bronchiolitis and unclassified lower respiratory tract infections, respectively. Of the 551 (55%) with documented viral infection, a single virus was detected in 491 (89%), including rhinovirus (n = 169; 34%), respiratory syncytial virus (n = 167; 34%), parainfluenza virus (n = 40; 8%), human metapneumovirus (n = 39; 8%), influenza virus (n = 31; 6%), bocavirus (n = 16; 3%), adenovirus (n = 15; 3%), coronavirus (n = 9; 2%) and enterovirus (n = 5; 1%). Coinfections with multiple viruses were detected in 6% (2 viruses detected in 59 cases; 3 viruses detected in 1 case).

CONCLUSION

Similar to other tropical countries, rhinovirus and respiratory syncytial virus were the principal viral pathogens detected among children hospitalized for lower tract respiratory infection in Cambodia.

Incidence of respiratory viruses in patients with community-acquired pneumonia admitted to the intensive care unit: results from the Severe Influenza Pneumonia Surveillance (SIPS) project

Few patients with community-acquired pneumonia (CAP) require admission to the intensive care unit (ICU-CAP). However, they represent the most severe form of the disease. An understanding of the etiologic agents of ICU-CAP may lead to better treatment decisions and patient outcomes. The objective of this study was to determine the incidence of respiratory viruses in patients with ICU-CAP. This was an observational study conducted in six Kentucky hospitals from December 2008 through October 2011. A case of ICU-CAP was defined as a patient admitted to an ICU with the diagnosis of CAP. The Luminex xTAG multiplex polymerase chain reaction (PCR) assay was used for viral identification. A total of 468 adult and pediatric patients with ICU-CAP were enrolled in the study. A total of 92 adult patients (23 %) and 14 pediatric patients (19 %) had a respiratory virus identified. Influenza was the most common virus identified in adults and the second most common in pediatric patients. This study suggests that respiratory viruses may be common etiologic agents of pneumonia in patients with ICU-CAP. The Centers for Disease Control and Prevention (CDC) recommend empiric anti-influenza therapy during the winter for hospitalized patients with CAP. This study supports this recommendation in patients with ICU-CAP.