Severe Acute Respiratory Illness Deaths in Sub-Saharan Africa and the Role of Influenza: A Case Series From 8 Countries

Characterizing deaths among adult patients with severe acute respiratory infection: during the pre- and COVID-19 pandemic periods in Bangladesh, 2018-2022

BACKGROUND

Severe acute respiratory infection (SARI) is a leading cause of mortality globally, peaking during the COVID-19 pandemic. We analyzed SARI-associated deaths during the pre-and-pandemic periods in Bangladesh to identify the contributing factors.

METHODS

We analyzed data from hospital-based influenza surveillance at nine tertiary-level hospitals in Bangladesh. We considered March 2018-February 2020 as the pre-pandemic period and March 2020-February 2022 as the pandemic period and included adult (≥ 18 years) participants in our study. Surveillance physicians identified WHO-SARI case definition meeting inpatients and collected demographics, clinical characteristics, and outcomes at hospital discharge and 30 days post-discharge. We performed rRT-PCR for influenza and SARS-CoV-2 viruses on collected nasopharyngeal and oropharyngeal swabs. We used multivariable Cox's regression models to calculate the hazard ratio (HR) for factors associated with SARI deaths in these adult patients.

RESULTS

We enrolled 4392 SARI patients during the pre-pandemic and 3824 SARI patients during the pandemic period. Case fatality ratio was higher during the pandemic: 13.62% (521) [in-hospital: 6.45% (247); post-discharge: 7.17% (274)] compared to pre-pandemic, 6.01% (264) [in-hospital: 2.01% (89), post-discharge: 4% (175)] (p < 0.001). Pre-pandemic, influenza was detected in 14% (37/264) of SARI deaths. Influenza was detected during the pandemic in 2.3% (12/521), SARS-CoV-2 in 41.8% (218/521), and both viruses in only one SARI death. History of smoking and the presence of 1 or more co-morbid conditions independently attributed to SARI deaths in adults in the pre-pandemic period. SARI deaths in such patients were also associated with respiratory difficulties on admission in both pre-pandemic (aHR 2.36; 95% CI:1.65-3.36) and pandemic period (aHR 2.30; 95% CI: 1.57-3.35) after accounting for age, sex, smoking status, presence of 1 or more co-morbid conditions, and detection of influenza and SARS-CoV-2 viruses.

CONCLUSIONS

During the pandemic, SARI mortality increased; influenza-associated mortality declined, and SARS-CoV-2 caused over a third of SARI deaths. Post-discharge mortality was higher than in-hospital mortality during both periods. Limiting premature discharge and strengthening post-discharge monitoring and nursing services could reduce unexpected deaths. Formative research to better understand post-discharge mortality is essential to reduce SARI deaths.

Effect of antipyretics on performance of influenza surveillance in Ghana

BACKGROUND

The World Health Organization's case definition for influenza-like illness (ILI) includes a measured temperature of ≥38°C. We conducted this study to assess the effect of antipyretics on performance of ILI surveillance in Ghana.

METHODS

A cross-sectional study was conducted in two districts of Ghana from September 2013 to May 2014. We collected epidemiological data and respiratory specimens from an expanded ILI case definition, which included patients presenting to health facilities with measured temperature ≥38°C or reported fever (but afebrile at the time of evaluation), and cough, with onset in the last 10 days. Specimens were tested for influenza viruses by real time reverse-transcription polymerase chain reaction.

RESULTS

Of 321 participants who met our expanded ILI case definition, 236 presented with temperature of <38°C but reported subjective fever. Of these, 17% (39/236) were positive for influenza virus; Of those with fever ≤38°C who took antipyretics, 21%(16/77) were positive for influenza, compared with 14%(23/159) of those who did not take antipyretics. The addition of subjective fever to the standard ILI case definition captured approximately an additional 57% influenza cases but also required testing of approximately four times as many patients. However, including those without fever on presentation that had taken antipyretics found an additional 23% of Influenza cases and only two times as much testing.

CONCLUSION

Depending on the goals of surveillance (monitoring virus circulation or determining disease burden) and available resources, a more sensitive case definition including subjective fever and history of use of antipyretics may be warranted.

Prevalence and Characteristics of Malaria and Influenza Co-Infection in Febrile Patients: A Systematic Review and Meta-Analysis

Malaria and influenza are co-endemic in several geographical areas, and differentiation of their clinical features is difficult. The present study aimed to qualitatively and quantitatively analyze the prevalence and characteristics of malaria and influenza co-infection in febrile patients. The systematic review was registered at PROSPERO (CRD42021264525). Relevant literature that reported malaria and influenza co-infection in febrile patients were searched in PubMed, Web of Science, and Scopus from 20 June to 27 June 2021 and the risk of bias for each study was assessed. Quantitative analysis included pooled prevalence, and the odds of malaria and influenza virus co-infection among febrile patients were estimated using a random-effects model. Subgroup analyses were performed to summarize the effect estimate for each group. Funnel plot, Egger’s test, and contour-enhanced funnel plot were used to demonstrate any publication bias among outcomes of included studies. Among 4253 studies retrieved, 10 studies that enrolled 22,066 febrile patients with 650 co-infected patients were included for qualitative and quantitative syntheses. The pooled prevalence of malaria and influenza virus co-infection among febrile patients was 31.0% in Nigeria, 1.0% in Tanzania, 1.0% in Uganda, 1.0% in Malawi, 1.0% in Ghana, 0% in Cambodia, 7.0% in the Central African Republic, and 7.0% in Kenya. Meta-analysis also showed co-infection occurrence by chance (p = 0.097, odds ratio 0.54, 95% CI 0.26–1.12, I² 94.9%). The prevalence of malaria and influenza virus co-infection among febrile patients was heterogeneous by country, characteristics of febrile participants, and diagnostic tests for influenza virus. Further studies should investigate severe clinical manifestations or differentiate clinical outcomes between mono-infected or co-infected individuals, whether the co-infection leads to severe disease outcome.

Severe acute respiratory illness surveillance for influenza in Kenya: Patient characteristics and lessons learnt

Background

We describe the epidemiology and clinical features of Kenyan patients hospitalized with laboratory‐confirmed influenza compared with those testing negative and discuss the potential contribution of severe acute respiratory illness (SARI) surveillance in monitoring a broader range of respiratory pathogens.

Methods

We described demographic and clinical characteristics of SARI cases among children (<18 years) and adults, separately. We compared disease severity (clinical features and treatment) of hospitalized influenza positive versus negative cases and explored independent predictors of death among SARI cases using a multivariable logistic regression model.

Results

From January 2014 to December 2018, 11,166 persons were hospitalized with SARI and overall positivity for influenza was ~10%. There were 10,742 (96%) children (<18 years)—median age of 1 year, interquartile range (IQR = 6 months, 2 years). Only 424 (4%) of the SARI cases were adults (≥18 years), with median age of 38 years (IQR 28 years, 52 years). There was no difference in disease severity comparing influenza positive and negative cases among children. Children hospitalized with SARI who had an underlying illness had greater odds of in‐hospital death compared with those without (adjusted odds ratio 2.11 95% CI 1.09–4.07). No further analysis was done among adults due to the small sample size.

Conclusion

Kenya's sentinel surveillance for SARI mainly captures data on younger children. Hospital‐based platforms designed to monitor influenza viruses and associated disease burden may be adapted and expanded to other respiratory viruses to inform public health interventions. Efforts should be made to capture adults as part of routine respiratory surveillance.

Assessment of surveillance predictors for suspected respiratory syncytial virus, influenza and Streptococcus pneumoniae infections in children aged <5 years in Madagascar

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A sensitive surveillance case definition can be defined based on specific symptoms.

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Intercostal recession and dyspnoea may be used to identify children with respiratory syncytial virus (RSV) infection.

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Fever was not necessarily a good predictor of paediatric RSV infection.

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Headache may be used to identify influenza infection in children.

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Sweats and productive cough may define infection due to Streptococcus pneumoniae in children.

Background

The lack of rapid, sensitive and affordable diagnostic tests that can distinguish a wide variety of respiratory pathogens at the point of care is an obstacle to the rapid implementation of control measures following events and epidemics. In addition, the absence of a standardized case definition to differentiate putative aetiologies is a challenge to assessing the burden of disease. This study aimed to identify the clinical spectrum of respiratory pathogens commonly associated with respiratory tract infections in the context of disease surveillance.

Methods

Data obtained from prospective hospital-based severe acute respiratory infection surveillance among children aged <5 years from November 2010 to July 2013 were used in this study.

Results

Intercostal recession and dyspnoea were predictive of respiratory syncytial virus (RSV) infection, whereas headache and chills were more often observed during influenza A infection. Male patients were at a higher risk for RSV infection than female patients. Productive cough, chills, sweating and weight loss were significantly associated with Streptococcus pneumoniae infection. The presence of fever did not necessarily indicate RSV infection.

Conclusions

Combined with other examinations, this study shows the value of including the syndromic approach in the panel of diagnostic criteria for rapid identification of the risk of infectious diseases in areas where laboratory diagnostics are challenging. Given the current situation with coronavirus disease 2019, this approach may help decision makers to implement appropriate control measures.

Mortality in children aged <5 years with severe acute respiratory illness in a high HIV-prevalence urban and rural areas of South Africa, 2009-2013

BACKGROUND

Severe acute respiratory illness (SARI) is an important cause of mortality in young children, especially in children living with HIV infection. Disparities in SARI death in children aged <5 years exist in urban and rural areas.

OBJECTIVE

To compare the factors associated with in-hospital death among children aged <5 years hospitalized with SARI in an urban vs. a rural setting in South Africa from 2009-2013.

METHODS

Data were collected from hospitalized children with SARI in one urban and two rural sentinel surveillance hospitals. Nasopharyngeal aspirates were tested for ten respiratory viruses and blood for pneumococcal DNA using polymerase chain reaction. We used multivariable logistic regression to identify patient and clinical characteristics associated with in-hospital death.

RESULTS

From 2009 through 2013, 5,297 children aged <5 years with SARI-associated hospital admission were enrolled; 3,811 (72%) in the urban and 1,486 (28%) in the rural hospitals. In-hospital case-fatality proportion (CFP) was higher in the rural hospitals (6.9%) than the urban hospital (1.3%, p<0.001), and among HIV-infected than the HIV-uninfected children (9.6% vs. 1.6%, p<0.001). In the urban hospital, HIV infection (odds ratio (OR):11.4, 95% confidence interval (CI):5.4-24.1) and presence of any other underlying illness (OR: 3.0, 95% CI: 1.0-9.2) were the only factors independently associated with death. In the rural hospitals, HIV infection (OR: 4.1, 95% CI: 2.3-7.1) and age <1 year (OR: 3.7, 95% CI: 1.9-7.2) were independently associated with death, whereas duration of hospitalization ≥5 days (OR: 0.5, 95% CI: 0.3-0.8) and any respiratory virus detection (OR: 0.4, 95% CI: 0.3-0.8) were negatively associated with death.

CONCLUSION

We found that the case-fatality proportion was substantially higher among children admitted to rural hospitals and HIV infected children with SARI in South Africa. While efforts to prevent and treat HIV infections in children may reduce SARI deaths, further efforts to address health care inequality in rural populations are needed.

Epidemiology and Seasonality of Childhood Respiratory Syncytial Virus Infections in the Tropics

Infections caused by respiratory syncytial virus (RSV) are a major cause of morbidity and mortality in young children worldwide. Understanding seasonal patterns of region-specific RSV activity is important to guide resource allocation for existing and future treatment and prevention strategies. The decades of excellent RSV surveillance data that are available from the developed countries of the world are incredibly instructive in advancing public health initiatives in those regions. With few exceptions, these developed nations are positioned geographically across temperate regions of the world. RSV surveillance across tropical regions of the world has improved in recent years, but remains spotty, and where available, still lacks the necessary longitudinal data to determine the amount of seasonal variation expected over time. However, existing and emerging data collected across tropical regions of the world do indicate that patterns of infection are often quite different from those so well described in temperate areas. Here, we provide a brief summary regarding what is known about general patterns of RSV disease activity across tropical Asia, Africa and South America, then offer additional country-specific details using examples where multiple reports and/or more robust surveillance data have become available.

Spatial patterns of lower respiratory tract infections and their association with fine particulate matter

This study aimed to identify the spatial patterns of lower respiratory tract infections (LRIs) and their association with fine particulate matter (PM_2.5). The disability-adjusted life year (DALY) database was used to represent the burden each country experiences as a result of LRIs. PM_2.5 data obtained from the Atmosphere Composition Analysis Group was assessed as the source for main exposure. Global Moran's I and Getis-Ord Gi* were applied to identify the spatial patterns and for hotspots analysis of LRIs. A generalized linear mixed model was coupled with a sensitivity test after controlling for covariates to estimate the association between LRIs and PM_2.5. Subgroup analyses were performed to determine whether LRIs and PM_2.5 are correlated for various ages and geographic regions. A significant spatial auto-correlated pattern was identified for global LRIs with Moran's Index 0.79, and the hotspots of LRIs were clustered in 35 African and 4 Eastern Mediterranean countries. A consistent significant positive association between LRIs and PM_2.5 with a coefficient of 0.21 (95% CI 0.06-0.36) was identified. Furthermore, subgroup analysis revealed a significant effect of PM_2.5 on LRI for children (0-14 years) and the elderly (≥ 70 years), and this effect was confirmed to be significant in all regions except for those comprised of Eastern Mediterranean countries.

The epidemiology of seasonal influenza after the 2009 influenza pandemic in Africa: a systematic review

Background

Influenza infection is a serious public health problem that causes an estimated 3 to 5 million cases and 250,000 deaths worldwide every year. The epidemiology of influenza is well-documented in high- and middle-income countries, however minimal effort had been made to understand the epidemiology, burden and seasonality of influenza in Africa. This study aims to assess the state of knowledge of seasonal influenza epidemiology in Africa and identify potential data gaps for policy formulation following the 2009 pandemic.

Method

We reviewed articles from Africa published into four databases namely: MEDLINE (PubMed), Google Scholar, Cochrane Library and Scientific Research Publishing from 2010 to 2019.

Results

We screened titles and abstracts of 2070 studies of which 311 were selected for full content evaluation and 199 studies were considered. Selected articles varied substantially on the basis of the topics they addressed covering the field of influenza surveillance (n=80); influenza risk factors and co-morbidities (n=15); influenza burden (n=37); influenza vaccination (n=40); influenza and other respiratory pathogens (n=22) and influenza diagnosis (n=5).

Conclusion

Significant progress has been made since the last pandemic in understanding the influenza epidemiology in Africa. However, efforts still remain for most countries to have sufficient data to allow countries to prioritize strategies for influenza prevention and control.

Systematic analysis of infectious disease outcomes by age shows lowest severity in school-age children

The COVID-19 pandemic has ignited interest in age-specific manifestations of infection but surprisingly little is known about relative severity of infectious disease between the extremes of age. In a systematic analysis we identified 142 datasets with information on severity of disease by age for 32 different infectious diseases, 19 viral and 13 bacterial. For almost all infections, school-age children have the least severe disease, and severity starts to rise long before old age. Indeed, for many infections even young adults have more severe disease than children, and dengue was the only infection that was most severe in school-age children. Together with data on vaccine response in children and young adults, the findings suggest peak immune function is reached around 5-14 years of age. Relative immune senescence may begin much earlier than assumed, before accelerating in older age groups. This has major implications for understanding resilience to infection, optimal vaccine scheduling, and appropriate health protection policies across the life course.

An evaluation of the Zambia influenza sentinel surveillance system, 2011-2017

Background

Over the past decade, influenza surveillance has been established in several African countries including Zambia. However, information on the on data quality and reliability of established influenza surveillance systems in Africa are limited. Such information would enable countries to assess the performance of their surveillance systems, identify shortfalls for improvement and provide evidence of data reliability for policy making and public health interventions.

Methods

We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza surveillance system (ISS) in Zambia during 2011–2017 using 9 attributes: (i) data quality and completeness, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability, (viii) utility, and (ix) sustainability. Each attribute was evaluated using pre-defined indicators. For each indicator we obtained the proportion (expressed as percentage) of the outcome of interest over the total. A scale from 1 to 3 was used to provide a score for each attribute as follows: < 60% (as obtained in the calculation above) scored 1 (weak performance); 60–79% scored 2 (moderate performance); ≥80% scored 3 (good performance). An overall score for each attribute and the ISS was obtained by averaging the scores of all evaluated attributes.

Results

The overall mean score for the ISS in Zambia was 2.6. Key strengths of the system were the quality of data generated (score: 2.9), its flexibility (score: 3.0) especially to monitor viral pathogens other than influenza viruses, its simplicity (score: 2.8), acceptability (score: 3.0) and stability (score: 2.6) over the review period and its relatively low cost ($310,000 per annum). Identified weaknesses related mainly to geographic representativeness (score: 2.0), timeliness (score: 2.5), especially in shipment of samples from remote sites, and sustainability (score: 1.0) in the absence of external funds.

Conclusions

The system performed moderately well in our evaluation. Key improvements would include improvements in the timeliness of samples shipments and geographical coverage. However, these improvements would result in increased cost and logistical complexity. The ISSS in Zambia is largely reliant on external funds and the acceptability of maintaining the surveillance system through national funds would require evaluation.

Evaluation of the influenza sentinel surveillance system in the Democratic Republic of Congo, 2012-2015

BACKGROUND

The World Health Organization recommends periodic evaluations of influenza surveillance systems to identify areas for improvement and provide evidence of data reliability for policymaking. However, data about the performance of established influenza surveillance systems are limited in Africa, including in the Democratic Republic of Congo (DRC).

METHODS

We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza sentinel surveillance system (ISSS) in DRC during 2012-2015. The performance of the system was evaluated using eight surveillance attributes: (i) data quality and completeness for key variables, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability and (viii) utility. For each attribute, specific indicators were developed and described using quantitative and qualitative methods. Scores for each indicator were as follows: < 60% weak performance; 60-79% moderate performance; ≥80% good performance.

RESULTS

During 2012-2015, we enrolled and tested 4339 patients with influenza-like illness (ILI) and 2869 patients with severe acute respiratory illness (SARI) from 11 sentinel sites situated in 5 of 11 provinces. Influenza viruses were detected in 446 (10.3%) samples from patients with ILI and in 151 (5.5%) samples from patients with SARI with higher detection during December-May. Data quality and completeness was > 90% for all evaluated indicators. Other strengths of the system were timeliness, simplicity, stability and utility that scored > 70% each. Representativeness, flexibility and acceptability had moderate performance. It was reported that the ISSS contributed to: (i) a better understanding of the epidemiology, circulating patterns and proportional contribution of influenza virus among patients with ILI or SARI; (ii) acquisition of new key competences related to influenza surveillance and diagnosis; and (iii) continuous education of surveillance staff and clinicians at sentinel sites about influenza. However, due to limited resources no actions were undertaken to mitigate the impact of seasonal influenza epidemics.

CONCLUSIONS

The system performed overall satisfactorily and provided reliable and timely data about influenza circulation in DRC. The simplicity of the system contributed to its stability. A better use of the available data could be made to inform and promote prevention interventions especially among the most vulnerable groups.

Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016

In 2010, Yemen started the surveillance for severe acute respiratory infections (SARIs) by establishing 2 sentinel sites in Sana’a and Aden city. This study aims to determine the proportions of influenza and noninfluenza viruses among SARI patients and to determine the severity of SARI and its associated factors. The data of SARI patients who were admitted to SARI surveillance sites at Al Johory hospital in Sana’a and Al Wahdah hospital in Aden city during the period 2011-2016 were analyzed. The proportions of positive influenza viruses (type A, B) and noninfluenza viruses (respiratory syncytial, adenovirus, human parainfluenza, and human metapneumovirus), intensive care unit (ICU) admission rate, and fatality rate among SARI patients were calculated. A total of 1811 of SARI patients were admitted during 2011-2016. Of those, 78% were <15 years old. A total of 89 (5%) patients had influenza viruses and 655 (36%) had noninfluenza viruses. The overall ICU admission rate was 40% and the case-fatality rate was 8%. Infection by influenza type (A, B) and mixed (adenovirus, human parainfluenza) was significantly associated with lower ICU admission. Age <15 years old, infection with influenza B, pre-existence of chronic diseases, and admission to Aden site were significantly associated with higher fatality rate among patients. In conclusion; SARI patients in Yemen had a high ICU admission and case-fatality rates. Influenza type B, chronic diseases, and admission to Aden site are associated with higher fatality rate. Expanding surveillance sites and panel of laboratory tests to involve other pathogens will help to provide accurate diagnosis for SARI etiology and give more comprehensive picture. Training staff for SARI case management will help to reduce severe outcomes.

Early T Cell Differentiation with Well-Maintained Function across the Adult Life Course in Sub-Saharan Africa

Immune senescence is a significant contributor to health problems in the developed world and may be accelerated by chronic viral infections. To date, there have been few studies of immune function in healthy older people in sub-Saharan Africa. We assessed T cell and B cell phenotypes and immune responses to CMV, EBV, and influenza virus in Malawians aged 20-69 y. Notably, the proportion of naive (CCR7⁺CD45RA⁺) CD4 and CD8 T cells was only 14% of the lymphoid repertoire even in donors aged under 30 y but did not decrease further with age. A small increase in the late differentiated (CD27^-CD28^-) CD8 T cell subpopulation was observed in older donors but the CD4/CD8 T cell ratio remained stable in all age groups. Interestingly, the regulatory (CD25^hiFOXP3^hi) T cell subpopulation was small in all age groups, and we observed no age-associated accumulation of cells expressing the senescence- and exhaustion-associated markers CD57 and PD-1. We assessed functional T cell responses to mitogenic and viral antigenic stimulation by the expression of CD154, IFN-γ, TNF-α, IL-2, and IL-17 and proliferation. All responses were robust across the life course, although we observed an age-associated shift from IFN-γ to TNF-α in the response to EBV. In summary, we found the naive T cell subpopulation of young adult Malawians was smaller than in their contemporaries in high-income settings but remains stable thereafter and that lymphocyte function is retained across the life course. These observations indicate that studies of the genetic and environmental factors influencing immune function in different environments may provide insights into minimizing immune ageing.

Dust or disease? Perceptions of influenza in rural Southern Malawi

Influenza virus infections cause between 291 243 and 645 832 deaths annually, with the highest burden in low-income settings. Research in high-income countries has examined public understanding of influenza, but there is little information on views and behaviours about influenza in low-income countries. We explored communities' ideas about the severity, causes, prevention and treatment of influenza in Chikwawa district, Malawi. We conducted 64 in-depth interviews with parents of children aged <5 years, and 7 focus groups with community health workers, parents, and traditional healers. Data were analysed thematically and using a framework matrix to compare views between groups. Respondents held varied ideas about influenza, and many were uncertain about its causes and treatment. Some parents, traditional healers and health workers thought influenza was not severe because they felt it did not cause death or limit activities, but others disagreed. Many saw influenza as a symptom of other conditions, especially malaria and pneumonia, rather than as a disease of its own. Most mentioned dust as the main cause of influenza and believed influenza could be prevented by cleaning the home thoroughly. Treatment seeking for influenza followed different stages, usually starting with home remedies followed by purchasing drugs from groceries and then visiting a health centre. Seeking a clinician tended to be triggered by severe symptoms like high fever or difficulty breathing, and suspicions of malaria or pneumonia. Community health workers provide health education for communities, but some lacked understanding of influenza. Our findings suggest uncertainty about the causes and control of influenza among parents and varied levels of understanding among health providers. Strengthening the capacity of community health workers to provide relevant information about influenza prevention and treatment could address parents' interest in further information and support informed health seeking and engagement with future influenza interventions.

Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013

BACKGROUND

Few comprehensive data exist regarding the epidemiology of severe acute respiratory infections (SARI) in low income countries. This study aimed at identifying etiologies and describing clinical features of SARI-associated hospitalization in Madagascar.

METHODS

It is a prospective surveillance of SARI in 2 hospitals for 3 years. Nasopharyngeal swabs, sputum, and blood were collected from SARI patients enrolled and tested for viruses and bacteria. Epidemiological and clinical information were obtained from case report forms.

RESULTS

Overall, 876 patients were enrolled in the study, of which 83.1% (728/876) were tested positive for at least one pathogen. Viral and bacterial infections occurred in 76.1% (667/876) and 35.8% (314/876) of tested samples, respectively. Among all detected viruses, respiratory syncytial virus (RSV) was the most common (37.7%; 348/924) followed by influenza virus A (FLUA, 18.4%; 170/924), rhinovirus (RV, 13.5%; 125/924), and adenovirus (ADV, 8.3%; 77/924). Among bacteria, Streptococcus pneumoniae (S. pneumoniae, 50.3%, 189/370) was the most detected followed by Haemophilus influenzae type b (Hib, 21.4%; 79/370), and Klebsiella (4.6%; 17/370). Other Streptococcus species were found in 8.1% (30/370) of samples. Compared to patients aged less than 5 years, older age groups were significantly less infected with RSV. On the other hand, patients aged more than 64 years (OR = 3.66) were at higher risk to be infected with FLUA, while those aged 15-29 years (OR = 3.22) and 30-64 years (OR = 2.39) were more likely to be infected with FLUB (influenza virus B).

CONCLUSION

The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Amongst young children, the demonstrated burden of RSV should guide clinicians for a better case management of children. These findings reveal the need to develop point-of-care tests to avoid overuse of antibiotics and to promote vaccine that could reduce drastically the RSV hospitalizations.

Trends, patterns and causes of respiratory disease mortality among inpatients in Tanzania, 2006-2015

OBJECTIVE

To determine the causes, patterns and trends of respiratory diseases-related deaths in hospitals of Tanzania 2006-2015.

METHODS

Retrospective study involving 39 hospitals. Medical records of patients who died in hospital were retrieved, reviewed and analysed. Sources of data were hospital admission registers, death registers and International Classification of Diseases report forms. Information on demographic characteristics, date of death, the immediate underlying cause of death and co-morbid conditions was collected.

RESULTS

Of the 247 976 deaths reported during the 10-year period, respiratory diseases accounted for 12.92% (n = 32 042). The majority of the respiratory mortality was reported among males (55.9%). Overall median age at death was 31 years with an interquartile range (IQR) of 1-47. Median age at death was significantly higher among males (35 years) than females (28 years) (P < 0.0001). Most deaths (37.8%) occurred in eastern Tanzania. About one-third (31.3%) of all respiratory mortality was reported among under-five children, being among girls than boys (34.3% vs. 28.9%, χ²  = 10.3, P < 0.0001). Adolescent and young adult females (15-29 years) had higher age-standardised mortality rates per 100 000 due respiratory diseases than males. Pneumonia (n = 16 639; 51.9%) and pulmonary tuberculosis (n = 9687; 30.2%) accounted for the majority of deaths due to respiratory diseases. Significantly more females (n = 7665; 54.5%) than males died from pneumonia (n = 8878; 49.8%; χ²  = 8.5, P < 0.0001). By contrast, significantly more males (n = 6024; 34%) than females (n = 3596; 26%; χ²  = 15.5, P < 0.0001) died of tuberculosis. The proportion of death due to tuberculosis declined from 32.8% in 2006-2010 to 7.9% in 2011-2015. However, there was a significant increase in the proportion of death due to pneumonia from 49.6% in 2006-2010 to 53.4% in 2011-2015. Co-morbid conditions contributed to 9.1% (2871/31 628) of all deaths due to respiratory diseases. The most common co-morbid condition was HIV which accounted for 1735 (60.4%) deaths and was more common among males (60.8%; n = 957) than among females (59.7%; n = 764).

CONCLUSIONS

Respiratory diseases account for a substantial proportion of all causes of hospital death in Tanzania. Pneumonia and tuberculosis contribute to more than three quarters of all deaths due to respiratory diseases. Since most major respiratory illnesses are avoidable, it is important to strengthen the capacity of the health delivery system in managing cases of respiratory diseases.

Complexities and dilemmas in community consultation on the design of a research project logo in Malawi

BACKGROUND

Community engagement on research design is widely highlighted as an important approach for ethical research. This article reports the experience of consulting with communities on the logo used for an influenza study in Malawi. The logo was designed for use on badges worn by study researchers, participant information sheets and other project documents, and could affect perceptions of the study and consequent engagement in the research.

METHODS

Four focus group discussions were conducted with populations targeted by the influenza study: pregnant women, people with HIV, mothers and community members. The focus groups incorporated a participatory matrix exercise focusing on key themes emerging from the discussions such as: attractiveness, comprehension, acceptability and suggestions for improvement. Findings from the focus groups were analyzed according to these key themes.

RESULTS

The consultation highlighted important benefits of discussion with communities on research design, including providing new perspectives and helping to avoid harm. For example, people living with HIV felt that one of the possible logos could increase stigma within communities. The experience also indicated potential challenges of consultation. In particular, there were contrasting perspectives among the groups, such that the consultation did not provide a clear answer about which logo should be selected.

CONCLUSIONS

Our experience adds to current evidence on community engagement by reporting on an area where there is less discussion of community consultation for design of a study logo. The consultation exercise reaffirmed the value of community engagement, but also the difficulty of relying on a brief consultation for decision-making in research design. Further ethical guidance is required on how to negotiate contradictory views during consultations.

Molecular characterization of human adenovirus associated with acute respiratory infections in Cameroon from 2011 to 2014

Background

Human adenoviruses (HAdVs) cause a wide range of diseases worldwide, including respiratory infections. Studies on HAdV molecular epidemiology are limited in Cameroon. The purpose of this study is to document the different types HAdV circulating in Cameroon in children with acute respiratory infections.

Methods

Nasopharyngeal swabs were collected from 811 children under 15 years from 2011 to 2014. The HAdV detection was assessed by semi-quantitative generic PCR r-gene®. The HAdV-positive samples were typed by amplification and sequencing of partial hexon gene and a real-time PCR. Demographic data were collected and analyzed. The infection and hospitalization risk factors were assessed thought the Chi-square test.

Results

A total of 137/220 HAdV-positive samples were amplified successfully. Six species of HAdV (Mastadenovirus A to F) were detected with B (108/220) and C (47/220) being the predominant strains. Hospitalization and age were significantly associated to HAdV-B and HAdV-C respectively. Phylogenetic analysis of HAdV-B3 virus (18) and B7 (5) shows a conserved and a significant temporal stability in relation to the reference sequence (99.1 to 100% of similarity).

Conclusion

This study reported HAdV species and types detected in children with acute respiratory infections in Cameroon between September 2011 and July 2014. These results support further evaluation of the spatio-temporal circulation pattern of HAdV species and types in Cameroon.

The national and provincial burden of medically attended influenza-associated influenza-like illness and severe acute respiratory illness in the Democratic Republic of Congo, 2013-2015

BACKGROUND

Estimates of influenza-associated outpatient consultations and hospitalizations are severely limited in low- and middle-income countries, especially in Africa.

METHODS

We conducted active prospective surveillance for influenza-like illness (ILI) and severe acute respiratory illness (SARI) at 5 healthcare facilities situated in Kinshasa Province during 2013-2015. We tested upper respiratory tract samples for influenza viruses using a reverse transcription-polymerase chain reaction assay. We estimated age-specific numbers and rates of influenza-associated ILI outpatient consultations and SARI hospitalizations for Kinshasa Province using a combination of administrative and influenza surveillance data. These estimates were extrapolated to each of the remaining 10 provinces accounting for provincial differences in prevalence of risk factors for pneumonia and healthcare-seeking behavior. Rates were reported per 100 000 population.

RESULTS

During 2013-2015, the mean annual national number of influenza-associated ILI outpatient consultations was 1 003 212 (95% Confidence Incidence [CI]: 719 335-1 338 050 - Rate: 1205.3; 95% CI: 864.2-1607.5); 199 839 (95% CI: 153 563-254 759 - Rate: 1464.0; 95% CI: 1125.0-1866.3) among children aged <5 years and 803 374 (95% CI: 567 772-1 083 291 - Rate: 1154.5; 95% CI: 813.1-1556.8) among individuals aged ≥5 years. The mean annual national number of influenza-associated SARI hospitalizations was 40 361 (95% CI: 24 014-60 514 - Rate: 48.5; 95% CI: 28.9-72.7); 25 452 (95% CI: 19 146-32 944 - Rate: 186.5; 95% CI: 140.3-241.3) among children aged <5 years and 14 909 (95% CI: 4868-27 570 - Rate: 21.4; 95% CI: 28.9-72.7) among individuals aged ≥5 years.

CONCLUSIONS

The burden of influenza-associated ILI outpatient consultations and SARI hospitalizations was substantial and was highest among hospitalized children aged <5 years.

Overview of three influenza seasons in Georgia, 2014-2017

BACKGROUND

Influenza epidemiological and virologic data from Georgia are limited. We aimed to present Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) surveillance data and characterize influenza viruses circulating in the country over three influenza seasons.

METHODS

We analyzed sentinel site ILI and SARI data for the 2014-2017 seasons in Georgia. Patients' samples were screened by real-time RT-PCR and influenza viruses isolated were characterized antigenically by haemagglutination inhibition assay and genetically by sequencing of HA and NA genes.

RESULTS

32% (397/1248) of ILI and 29% (581/1997) of SARI patients tested were positive for influenza viruses. In 2014-2015 the median week of influenza detection was week 7/2015 with B/Yamagata lineage viruses dominating (79%); in 2015-2016-week 5/2016 was the median with A/H1N1pdm09 viruses prevailing (83%); and in 2016-2017 a bimodal distribution of influenza activity was observed-the first wave was caused by A/H3N2 (55%) with median week 51/2016 and the second by B/Victoria lineage viruses (45%) with median week 9/2017. For ILI, influenza virus detection was highest in children aged 5-14 years while for SARI patients most were aged >15 years and 27 (4.6%) of 581 SARI cases died during the three seasons. Persons aged 30-64 years had the highest risk of fatal outcome, notably those infected with A/H1N1pdm09 (OR 11.41, CI 3.94-33.04, p<0.001). A/H1N1pdm09 viruses analyzed by gene sequencing fell into genetic groups 6B and 6B.1; A/H3N2 viruses belonged to genetic subclades 3C.3b, 3C.3a, 3C.2a and 3C.2a1; B/Yamagata lineage viruses were of clade 3 and B/Victoria lineage viruses fell in clade1A.

CONCLUSION

In Georgia influenza virus activity occurred mainly from December through March in all seasons, with varying peak weeks and predominating viruses. Around one third of ILI/ SARI cases were associated with influenza caused by antigenically and genetically distinct influenza viruses over the course of the three seasons.

Epidemiology and molecular characterization of influenza viruses in Burkina Faso, sub-Saharan Africa

Background

The importance of influenza viruses in respiratory infections in sub‐Saharan Africa has been historically overlooked, including in Burkina Faso.

Objectives

This study therefore aimed at evaluating the prevalence and seasonal occurrence of influenza viruses in children under 5 years old, at risk of influenza‐related complications, presenting with influenza‐like illness (ILI) or severe acute respiratory infection (SARI). The study also aimed at identifying the periods with increased influenza transmission for vaccination recommendations in Burkina Faso.

Methods

From January 2014 to December 2015, ILI and SARI (2015 only) patients were recruited in six healthcare centers in Burkina Faso. Influenza A and B molecular detection and subtyping were performed. Clade clustering of a subset of A(H1N1)pdm09 and A(H3N2) strains was deduced by performing phylogenetic analyses on hemagglutinin gene sequences. Weekly surveillance data from FluNet (2011‐2013; 2016) and this study (2014‐2015) were used to identify periods of increased influenza activity.

Results

Influenza A and B viruses were detected in 15.1% (112 of 743) of ILI and 6.6% (12 of 181) of SARI patients. Overall, influenza A viruses were largely predominant (81 of 124, 65.3%), with 69.1% of A(H3N2) and 30.9% of A(H1N1)pdm09 strains. Four waves of increased transmission were identified in 2014‐2015, each dominated by different influenza subtypes and clades. Between 2011 and 2016, periods of increased influenza activity varied in their frequency, duration, and timing.

Conclusion

Influenza A and B viruses were detected in a substantial number of ILI and SARI cases in Burkina Faso. Vaccination in September‐October would likely protect the highest number of patients.

Clinical and epidemiological characterization of influenza virus infections in children with severe acute respiratory infection in Maputo, Mozambique: Results from the implementation of sentinel surveillance, 2014 - 2016

In Sub-Saharan Africa, where burden, impact, and incidence of acute respiratory infections (ARI) are the highest in the world, conversely, the epidemiology of influenza-associated severe acute respiratory infections (SARI) is incompletely known. The aim of this study was to describe the clinical and epidemiological features of influenza-associated SARI in hospitalized children in Maputo city, Mozambique. Nasopharyngeal and oropharyngeal swabs were collected from children aged 0-14 years old who met the case definition for SARI in two hospitals in Maputo city after their parents or legal representative consented to participate. A structured questionnaire was used to collect clinical and demographic data. Typing and subtyping of influenza were performed by real-time PCR. From January 2014 to December 2016, a total of 2,007 eligible children were recruited, of whom 1,997 (99.5%) were screened for influenza by real-time PCR. The median age of participants was 16.9 months (IQR: 7.0-38.9 months) and 53.9% (1076/1991) were male. A total of 77 were positive for influenza, yielding a frequency of 3.9% (77/1,991), with the highest frequency being reported in the age group 1-5 years old. Cases of influenza peaked twice each year, during which, its frequency reached up to 60%-80%. Among all influenza confirmed cases, 33.7% (26/77), 35.1% (27/77) and 28.6% (22/77) were typed as influenza A/H3N2, A/H1N1pdm09, and B, respectively. This represents the first report of influenza in urban/sub urban setting in Mozambique and the first evidence of distribution of strains of influenza in the country. Our data showed that frequency of influenza was lower than reported in a rural setting in Mozambique and the frequency of seasonal (A/H1N1pdm09) and (A/H3N2) subtypes were similar in children with SARI.

Transmission dynamics of influenza in two major cities of Uganda

In this paper, we report the epidemic characteristics of the three co-circulating influenza viruses (i.e., A/H1N1, A/H3N2, and B) in two tropical African cities-Kampala and Entebbe, Uganda-over an eight-year period (2008-2015). Using wavelet methods, we show that influenza epidemics recurred annually during the study period. In most months, two or more influenza viruses co-circulated at the same time. However, the epidemic timing differed by influenza (sub)type. Influenza A/H3N2 caused epidemics approximately every 2 years in both cities and tended to alternate with A/H1N1 or B. Influenza A/H1N1 and B produced smaller but more frequent epidemics and biennial epidemics of these two viruses tended to be synchronous. In addition, epidemics of A/H3N2 were more synchronized in the two cities (located ca.37 km apart) than that of A/H1N1 or influenza B.

Mortality estimates among adult patients with severe acute respiratory infections from two sentinel hospitals in southern Arizona, United States, 2010-2014

BACKGROUND

From October 2010 through February 2016, Arizona conducted surveillance for severe acute respiratory infections (SARI) among adults hospitalized in the Arizona-Mexico border region. There are few accurate mortality estimates in SARI patients, particularly in adults ≥ 65 years old. The purpose of this study was to generate mortality estimates among SARI patients that include deaths occurring shortly after hospital discharge and identify risk factors for mortality.

METHODS

Patients admitted to two sentinel hospitals between 2010 and 2014 who met the SARI case definition were enrolled. Demographic data were used to link SARI patients to Arizona death certificates. Mortality within 30 days after the date of admission was calculated and risk factors were identified using logistic regression models.

RESULTS

Among 258 SARI patients, 47% were females, 51% were white, non-Hispanic and 39% were Hispanic. The median age was 63 years (range, 19 to 97 years) and 80% had one or more pre-existing health condition; 9% died in hospital. Mortality increased to 12% (30/258, 30% increase) when electronic vital records and a 30-day post-hospitalization time frame were used. Being age ≥ 65 years (OR = 4.0; 95% CI: 1.6-9.9) and having an intensive care unit admission (OR = 7.4; 95% CI: 3.0-17.9) were independently associated with mortality.

CONCLUSION

The use of electronic vital records increased SARI-associated mortality estimates by 30%. These findings may help guide prevention and treatment measures, particularly in high-risk persons in this highly fluid border population.

Prevention and treatment of respiratory viral infections: Presentations on antivirals, traditional therapies and host-directed interventions at the 5th ISIRV Antiviral Group conference

The International Society for Influenza and other Respiratory Virus Diseases held its 5th Antiviral Group (isirv-AVG) Conference in Shanghai, China, in conjunction with the Shanghai Public Health Center and Fudan University from 14-16 June 2017. The three-day programme encompassed presentations on some of the clinical features, management, immune responses and virology of respiratory infections, including influenza A(H1N1)pdm09 and A(H7N9) viruses, MERS-CoV, SARS-CoV, adenovirus Type 80, enterovirus D68, metapneumovirus and respiratory syncytial virus (RSV). Updates were presented on several therapeutics currently in clinical trials, including influenza polymerase inhibitors pimodivir/JNJ6362387, S033188, favipiravir, monoclonal antibodies MHAA45449A and VIS410, and host directed strategies for influenza including nitazoxanide, and polymerase ALS-008112 and fusion inhibitors AK0529, GS-5806 for RSV. Updates were also given on the use of the currently licensed neuraminidase inhibitors. Given the location in China, there were also presentations on the use of Traditional Chinese Medicines. Following on from the previous conference, there were ongoing discussions on appropriate endpoints for severe influenza in clinical trials from regulators and clinicians, an issue which remains unresolved. The aim of this conference summary is to provide information for not only conference participants, but a detailed referenced review of the current status of clinical trials, and pre-clinical development of therapeutics and vaccines for influenza and other respiratory diseases for a broader audience.

The national burden of influenza-associated severe acute respiratory illness hospitalization in Zambia, 2011-2014

BACKGROUND

Estimates of influenza-associated hospitalization are limited in low- and middle-income countries, especially in Africa.

OBJECTIVE

To estimate the national number of influenza-associated severe acute respiratory illness (SARI) hospitalization in Zambia.

METHODS

We conducted active prospective hospital-based surveillance for SARI at the University Teaching Hospital (UTH) situated in Lusaka Province during 2011-2014. Upper respiratory tract samples were tested for influenza virus using a reverse transcriptase polymerase chain reaction assay. We estimated age-specific rates of influenza-associated SARI hospitalizations for the UTH using census and secondary data on respiratory hospitalizations following estimation approaches recommended by the World Health Organization. We used the UTH hospitalization rates as a proxy for Lusaka Province. These rates were adjusted for each of the remaining 9 provinces based on their prevalence of risk factors for pneumonia and healthcare-seeking behavior. Rates were expressed per 100,000 population.

RESULTS

SARI cases accounted for 77.1% (13 389/17 354) of respiratory admissions at the UTH; 82.7% (11 859/14 344) and 50.8% (1530/3010) among individuals aged <5 and ≥5 years, respectively. Among SARI cases tested, the influenza virus detection rate was 5.5% (152/2734), 4.8% (48/998), and 6.0% (104/1736) among individuals aged <5 and ≥5 years, respectively. The mean annual national number of influenza-associated SARI hospitalizations was 6181 (95% CI: 4321-8041-rate: 43.9; 95% CI: 30.7-57.1); 4669 (95% CI: 3287-6051-rate: 187.7; 95% CI: 132.1-243.3) among children aged <5 years; and 1512 (95% CI: 1037-1987-rate: 13.1; 95% CI: 9.0-17.2) among individuals aged ≥5 years.

CONCLUSIONS

The burden of influenza-associated SARI hospitalizations was substantial and was highest among children aged <5 years.

Report on eighth WHO meeting on development of influenza vaccines that induce broadly protective and long-lasting immune responses: Chicago, USA, 23-24 August 2016

In August 2016, the World Health Organization (WHO) convened the "Eighth meeting on development of influenza vaccines that induce broadly protective and long-lasting immune responses" to discuss the regulatory requirements and pathways for licensure of next-generation influenza vaccines, and to identify areas where WHO can promote the development of such vaccines. Participants included approximately 120 representatives of academia, the vaccine industry, research and development funders, and regulatory and public health agencies. They reviewed the draft WHO preferred product characteristics (PPCs) of vaccines that could address prioritized unmet public health needs and discussed the challenges facing the development of such vaccines, especially for low- and middle-income countries (LMIC). They defined the data desired by public-health decision makers globally and explored how to support the progression of promising candidates into late-stage clinical trials and for all countries. This report highlights the major discussions of the meeting.

Epidemiology of influenza in West Africa after the 2009 influenza A(H1N1) pandemic, 2010-2012

Background

Over the last decade, capacity for influenza surveillance and research in West Africa has strengthened. Data from these surveillance systems showed influenza A(H1N1)pdm09 circulated in West Africa later than in other regions of the continent.

Methods

We contacted 11 West African countries to collect information about their influenza surveillance systems (number of sites, type of surveillance, sampling strategy, populations sampled, case definitions used, number of specimens collected and number of specimens positive for influenza viruses) for the time period January 2010 through December 2012.

Results

Of the 11 countries contacted, 8 responded: Burkina Faso, Cote d’Ivoire, Mali, Mauritania, Niger, Nigeria, Sierra Leone and Togo. Countries used standard World Health Organization (WHO) case definitions for influenza-like illness (ILI) and severe acute respiratory illness (SARI) or slight variations thereof. There were 70 surveillance sites: 26 SARI and 44 ILI. Seven countries conducted SARI surveillance and collected 3114 specimens of which 209 (7%) were positive for influenza viruses. Among influenza-positive SARI patients, 132 (63%) were influenza A [68 influenza A(H1N1)pdm09, 64 influenza A(H3N2)] and 77 (37%) were influenza B. All eight countries conducted ILI surveillance and collected 20,375 specimens, of which 2278 (11%) were positive for influenza viruses. Among influenza-positive ILI patients, 1431 (63%) were influenza A [820 influenza A(H1N1)pdm09, 611 influenza A(H3N2)] and 847 (37%) were influenza B. A majority of SARI and ILI case-patients who tested positive for influenza (72% SARI and 59% ILI) were children aged 0–4 years, as were a majority of those enrolled in surveillance. The seasonality of influenza and the predominant influenza type or subtype varied by country and year.

Conclusions

Influenza A(H1N1)pdm09 continued to circulate in West Africa along with influenza A(H3N2) and influenza B during 2010–2012. Although ILI surveillance systems produced a robust number of samples during the study period, more could be done to strengthen surveillance among hospitalized SARI case-patients. Surveillance systems captured young children but lacked data on adults and the elderly. More data on risk groups for severe influenza in West Africa are needed to help shape influenza prevention and clinical management policies and guidelines.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2839-1) contains supplementary material, which is available to authorized users.

Respiratory syncytial and influenza viruses in children under 2 years old with severe acute respiratory infection (SARI) in Maputo, 2015

Introduction

Although respiratory syncytial virus (RSV) and influenza virus (influenza) infections are one of the leading causes of Severe Acute Respiratory Infections (SARI) and death in young children worldwide, little is known about the burden of these pathogens in Mozambique.

Material and methods

From January 2015 to January 2016, nasopharyngeal swabs from 450 children, aged ≤2 years, who had been admitted to the Pediatric Department of the Maputo Central Hospital (HCM) in Mozambique, suffering with SARI were enrolled and tested for influenza and RSV using a real-time PCR assay.

Results

Influenza and RSV were detected in 2.4% (11/450) and 26.7% (113/424) of the participants. Children with influenza were slightly older than those infected with RSV (10 months in influenza-infected children compared to 3 months in RSV-infected children); male children were predominant in both groups (63.6% versus 54.9% in children with influenza and RSV, respectively). There was a trend towards a higher frequency of influenza (72.7%) and RSV (93.8%) cases in the dry season. Bronchopneumonia, bronchitis and respiratory distress were the most common diagnoses at admission. Antibiotics were administered to 27,3% and 15,9% of the children with influenza and RSV, respectively. Two children, of whom, one was positive for RSV (aged 6 months) and another was positive for Influenza (aged 3 months) died; both were children of HIV seropositive mothers and had bronchopneumonia.

Conclusions

Our data demonstrated that RSV, and less frequently influenza, occurs in children with SARI in urban/sub-urban settings from southern Mozambique. The occurrence of deaths in small children suspected of being HIV-infected, suggests that particular attention should be given to this vulnerable population. Our data also provide evidence of antibiotics prescription in children with respiratory viral infection, which represents an important public health problem and calls for urgent interventions.

Theory and strategy for Pneumococcal vaccines in the elderly

Pneumonia is the fourth-leading cause of death globally, and Streptococcus pneumoniae is the most important causative pathogen. Because the incidence of pneumococcal diseases is likely to increase with the aging society, we should determine an optimal strategy for pneumococcal vaccination. While consensus indicates that 23-valent pneumococcal polysaccharide vaccine prevents invasive pneumococcal diseases (IPD), its effects on community-acquired pneumonia (CAP) remain controversial. Recently, a 13-valent pneumococcal conjugate vaccine (PCV13) was released. The latest clinical study (CAPiTA study) showed that PCV13 reduced vaccine-type CAP and IPD. Based on these results, the Advisory Committee on Immunization Practices recommended initial vaccination with PCV13 for the elderly. Scientific evidence regarding immunosenescence is needed to determine a more ideal vaccination strategy for the elderly with impaired innate and adaptive immunity. Continuing research on the cost effectiveness of new vaccine strategies considering constantly changing epidemiology is also warranted.

Mortality amongst patients with influenza-associated severe acute respiratory illness, South Africa, 2009-2013

INTRODUCTION

Data on the burden and risk groups for influenza-associated mortality from Africa are limited. We aimed to estimate the incidence and risk-factors for in-hospital influenza-associated severe acute respiratory illness (SARI) deaths.

METHODS

Hospitalised patients with SARI were enrolled prospectively in four provinces of South Africa from 2009-2013. Using polymerase chain reaction, respiratory samples were tested for ten respiratory viruses and blood for pneumococcal DNA. The incidence of influenza-associated SARI deaths was estimated at one urban hospital with a defined catchment population.

RESULTS

We enrolled 1376 patients with influenza-associated SARI and 3% (41 of 1358 with available outcome data) died. In patients with available HIV-status, the case-fatality proportion (CFP) was higher in HIV-infected (5%, 22/419) than HIV-uninfected individuals (2%, 13/620; p = 0.006). CFPs varied by age group, and generally increased with increasing age amongst individuals >5 years (p<0.001). On multivariable analysis, factors associated with death were age-group 45-64 years (odds ratio (OR) 4.0, 95% confidence interval (CI) 1.01-16.3) and ≥65 years (OR 6.5, 95%CI 1.2-34.3) compared to 1-4 year age-group who had the lowest CFP, HIV-infection (OR 2.9, 95%CI 1.1-7.8), underlying medical conditions other than HIV (OR 2.9, 95%CI 1.2-7.3) and pneumococcal co-infection (OR 4.1, 95%CI 1.5-11.2). The estimated incidence of influenza-associated SARI deaths per 100,000 population was highest in children <1 year (20.1, 95%CI 12.1-31.3) and adults aged 45-64 years (10.4, 95%CI 8.4-12.9). Adjusting for age, the rate of death was 20-fold (95%CI 15.0-27.8) higher in HIV-infected individuals than HIV-uninfected individuals.

CONCLUSION

Influenza causes substantial mortality in urban South Africa, particularly in infants aged <1 year and HIV-infected individuals. More widespread access to antiretroviral treatment and influenza vaccination may reduce this burden.