Influenza in Africa

Incidence of influenza virus-associated Severe Acute Respiratory Infections in three districts in 2018 at Gharbia governorate, Egypt

AIMS

Influenza remains a contributor to substantial global morbidity and mortality. There is very limited data on disease burden in Egypt. The purpose of this study was to estimate the incidence of influenza-associated Severe Acute Respiratory Illness (SARI) in three districts in Gharbia governorate in 2018.

METHODS

This study Followed the World Health Organization (WHO) manual for estimating disease burden associated with seasonal influenza. The hospital admission database was screened for SARI patients in three districts at Gharbia governorate in 2018. A hospital admission survey (HAS) was used to define the catchment population. The incidence rate estimation was computed as the number of influenza-positive SARI cases per 100,000 population.

RESULTS

A total of 180 SARI cases were identified in the catchment area. The median age was 23 years [IQR: 2-53], and 45% were males. Out of the total SARI cases, 33.3% influenza was confirmed by the laboratory test of RP-PCR. Influenza A(H3N2) virus predominated representing 55.0% of patients, thanA(H1N1) 26.7% and Flu-B virus 18.3%. Influenza prevailed in winter and spring; no deaths from influenza were reported. The annual incidence of influenza-associated SARIs found higher in <2 years (282 /100,000) and ≥65 years patients (215/100,000) at significant level p<0.001.

CONCLUSION

The WHO Manual for estimating disease burden associated with seasonal influenza was successfully operationalized in the three districts of Gharbia governorate. It can be used in other districts. A considerable burden was associated with influenza viruses requiring hospitalization, especially among the older adult group.

Shifting Patterns of Influenza Circulation during the COVID-19 Pandemic, Senegal

Historically low levels of seasonal influenza circulation were reported during the first years of the COVID-19 pandemic and were mainly attributed to implementation of nonpharmaceutical interventions. In tropical regions, influenza's seasonality differs largely, and data on this topic are scarce. We analyzed data from Senegal's sentinel syndromic surveillance network before and after the start of the COVID-19 pandemic to assess changes in influenza circulation. We found that influenza shows year-round circulation in Senegal and has 2 distinct epidemic peaks: during January-March and during the rainy season in August-October. During 2021-2022, the expected January-March influenza peak completely disappeared, corresponding to periods of active SARS-CoV-2 circulation. We noted an unexpected influenza epidemic peak during May-July 2022. The observed reciprocal circulation of SARS-CoV-2 and influenza suggests that factors such as viral interference might be at play and should be further investigated in tropical settings.

Acceptance and Risk Perception of COVID-19 Vaccination among Pregnant and Non Pregnant Women in Sub-Saharan Africa: A Cross-Sectional Matched-Sample Study

This study aims to evaluate the acceptance and risk perception of pregnant and non pregnant women towards COVID-19 vaccines using a cross-sectional matched-sample study approach. A web-based questionnaire with closed- and open-ended questions was administered to adults older than 18 years in the sub-Saharan African (SSA) region. Respondents (n = 131) were grouped based on their pregnancy status (54 pregnant and 77 non pregnant women) and matched for comparison by age. The matched groups were compared using the chi-square test and the t-test where appropriate. Compared to non pregnant women, pregnant women reported significantly lower risk perception scores of COVID-19 infection (3.74 vs. 5.78, p < 0.001) and were less likely to take the COVID-19 vaccine (odds ratio = 0.12, 95% confidence interval (CI) 0.06-0.27, p < 0.001). A similar proportion of pregnant and non pregnant women believed in false information about the COVID-19 vaccine, and 40% of unvaccinated pregnant women (n = 40) were concerned about the safety of the vaccine. After adjustment, women's education, marital status, belief in misconceptions and risk perception were associated with non-vaccination among pregnant women. The content analysis revealed that pregnant women refused the vaccine due to mistrust of their countries' health systems, concerns about the country where the vaccines were manufactured and a lack of confidence in the production process of the vaccines. This study shows the poor acceptance of COVID-19 vaccines among pregnant women in SSA, who perceived a lower risk of COVID-19 infection. Understanding the reasons for non-acceptance and the motivation to accept the COVID-19 vaccine could guide the development of health education and promotion programmes, and aid governments and policymakers in implementing targeted policy changes.

The burden of influenza among Kenyan pregnant and postpartum women and their infants, 2015–2020

Background

In tropical Africa, data about influenza‐associated illness burden are needed to assess potential benefits of influenza vaccination among pregnant women. We estimated the incidence of influenza among pregnant women and their infants in Siaya County, Kenya.

Methods

We enrolled women at <31 weeks of gestation and conducted weekly follow‐up until 6‐month postpartum to identify acute respiratory illnesses (ARIs). We defined ARI among mothers as reported cough, rhinorrhoea or sore throat and among infants as maternal‐reported cough, difficulty breathing, rhinorrhoea or clinician diagnosis of respiratory illness. We collected nasal/nasopharyngeal and oropharyngeal swabs from mothers/infants with ARI and tested for influenza A and B using molecular assays. We calculated antenatal incidence of laboratory‐confirmed influenza among mothers and postnatal incidence among mothers and infants.

Results

During June 2015 to May 2020, we analysed data from 3,026 pregnant women at a median gestational age of 16 weeks (interquartile range [IQR], 13, 18) and followed 2,550 infants. Incidence of laboratory‐confirmed influenza during pregnancy (10.3 episodes per 1,000 person‐months [95% confidence interval {CI} 8.6–11.8]) was twofold higher than in the postpartum period (4.0 [95% CI 2.6–5.5]; p < 0.01). Incidence was significantly higher among human immunodeficiency virus (HIV)‐infected pregnant women (15.6 [95% CI 11.0–20.6] vs. 9.1 [95% CI 7.5–10.8]; p < 0.01). Incidence among young infants was 4.4 (95% CI 3.0–5.9) and similar among HIV‐exposed and HIV‐unexposed infants.

Conclusion

Our findings suggest a substantial burden of influenza illnesses during pregnancy, with a higher burden among HIV‐infected mothers. Kenyan authorities should consider the value of vaccinating pregnant women, especially if HIV infected.

Global subtype diversity, spatial distribution patterns, and phylogenetic analysis of avian influenza virus in water

The current COVID-19 pandemic highlights the need for zoonotic infectious disease surveillance. Avian influenza virus (AIV) poses a significant threat to animal and public health due to its pandemic potential. Virus-contaminated water has been suggested as an important AIV spread mechanism among multiple species. Nevertheless, few studies have characterized the global AIV subtype diversity and distribution in environmental water. Therefore, this study aims to provide an updated descriptive and phylogenetic analysis of AIVs isolated in water samples from high risk-sites for influenza outbreaks (i.e. live bird markets, poultry farms, and wild bird habitats) on a global scale. The descriptive analysis evidenced that 21 subtypes were reported from nine countries between 2003 and 2020. Fourteen AIV subtypes were solely reported from Asian countries. Most of the viral sequences were obtained in China and Bangladesh with 47.44% and 23.93%, respectively. Likewise, the greatest global AIV subtype diversity was observed in China with 12 subtypes. Live bird markets represented the main sampling site for AIV detection in water samples (64.1%), mostly from poultry cage water. Nevertheless, the highest subtype diversity was observed in water samples from wild bird habitats, especially from the Izumi plain and the Dongting Lake located in Japan and China, respectively. Water from drinking poultry troughs evidenced the greatest subtype diversity in live bird markets; meanwhile, environmental water used by ducks had the highest number of different subtypes in poultry farms. Maximum-likelihood phylogenetic trees of hemagglutinin (HA) and neuraminidase (NA) genes showed that some sequences were closely related among different poultry/wild bird-related environments from different geographic origins. Therefore, the results suggest that even though the availability of gene sequences in public-access databases varies greatly among countries, environmental AIV surveillance represents a useful tool to elucidate potential viral diversity in wild and domestic bird populations.

Forecasting influenza-like illness trends in Cameroon using Google Search Data

Although acute respiratory infections are a leading cause of mortality in sub-Saharan Africa, surveillance of diseases such as influenza is mostly neglected. Evaluating the usefulness of influenza-like illness (ILI) surveillance systems and developing approaches for forecasting future trends is important for pandemic preparedness. We applied and compared a range of robust statistical and machine learning models including random forest (RF) regression, support vector machines (SVM) regression, multivariable linear regression and ARIMA models to forecast 2012 to 2018 trends of reported ILI cases in Cameroon, using Google searches for influenza symptoms, treatments, natural or traditional remedies as well as, infectious diseases with a high burden (i.e., AIDS, malaria, tuberculosis). The R2 and RMSE (Root Mean Squared Error) were statistically similar across most of the methods, however, RF and SVM had the highest average R2 (0.78 and 0.88, respectively) for predicting ILI per 100,000 persons at the country level. This study demonstrates the need for developing contextualized approaches when using digital data for disease surveillance and the usefulness of search data for monitoring ILI in sub-Saharan African countries.

Performance of case definitions and clinical predictors for influenza surveillance among patients followed in a rural cohort in Senegal

Background

Influenza is a major cause of morbidity and mortality in Africa. However, a lack of epidemiological data remains for this pathology, and the performances of the influenza-like illness (ILI) case definitions used for sentinel surveillance have never been evaluated in Senegal. This study aimed to i) assess the performance of three different ILI case definitions, adopted by the WHO, USA-CDC (CDC) and European-CDC (ECDC) and ii) identify clinical factors associated with a positive diagnosis for Influenza in order to develop an algorithm fitted for the Senegalese context.

Methods

All 657 patients with a febrile pathological episode (FPE) between January 2013 and December 2016 were followed in a cohort study in two rural villages in Senegal, accounting for 1653 FPE observations with nasopharyngeal sampling and influenza virus screening by rRT-PCR. For each FPE, general characteristics and clinical signs presented by patients were collected. Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) for the three ILI case definitions were assessed using PCR result as the reference test. Associations between clinical signs and influenza infection were analyzed using logistic regression with generalized estimating equations. Sore throat, arthralgia or myalgia were missing for children under 5 years.

Results

WHO, CDC and ECDC case definitions had similar sensitivity (81.0%; 95%CI: 77.0–85.0) and NPV (91.0%; 95%CI: 89.0–93.1) while the WHO and CDC ILI case definitions had the highest specificity (52.0%; 95%CI: 49.1–54.5) and PPV (32.0%; 95%CI: 30.0–35.0). These performances varied by age groups. In children < 5 years, the significant predictors of influenza virus infection were cough and nasal discharge. In patients from 5 years, cough, nasal discharge, sore throat and asthenia grade 3 best predicted influenza infection. The addition of “nasal discharge” as a symptom to the WHO case definition decreased sensitivity but increased specificity, particularly in the pediatric population.

Conclusion

In summary, all three definitions studies (WHO, ECDC & CDC) have similar performance, even by age group. The revised WHO ILI definition could be chosen for surveillance purposes for its simplicity. Symptomatic predictors of influenza virus infection vary according the age group.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-020-05724-x.

Falciparum Malaria in Febrile Patients at Sentinel Sites for Influenza Surveillance in the Central African Republic from 2015 to 2018

Malaria is a major public health issue in the Central African Republic (CAR) despite massive scale-up of malaria interventions. However, no information is available on the incidence of malaria in febrile illness cases or on the distribution of malaria infection according to demographic characteristics, which are important indicators and valuable epidemiological surveillance tools. This study therefore aimed to characterize malaria in the network of sentinel sites set up for influenza surveillance. A retrospective analysis was conducted to explore the data from these sentinel sites from 2015 to 2018. The Paracheck-Pf® rapid diagnosis test kit was used to screen for malaria in febrile illness cases. A total of 3609 malaria cases were identified in 5397 febrile patients, giving an incidence rate of 66.8%. The age group of 1–4 years was the most affected by malaria (76.0%). Moreover, prevalence varied across different sentinel sites, with the Bossembele Health Center, located in a rural area, showing an incidence of 96%, the Saint Joseph Health Center in a semiurban area of Bangui showing an incidence of 75%, and the Bangui Pediatric Complex in an urban site with an incidence of only 44.6%. Malaria transmission was holoendemic over the four-year study period, and malaria incidence decreased from 2016 to 2018. The incidence of malaria coinfection with influenza was 6.8%. This study demonstrated clear microspatial heterogeneity of malaria. Malaria was consistently the most frequent cause of febrile illness. Including sites in different climate zones in the CAR will allow for a more representative study.

COVID-19 au Sénégal: réflexion d´un microbiologiste

Les maladies respiratoires particulièrement le COVID-19 constituent un problème majeur de santé publique dans le monde. Depuis mars 2020, le Sénégal a enregistré 299 cas de COVID-19 dont 183 guéris et seulement deux cas sévères. Aussi environ 20000 personnes en contact étroit avec les malades ont été testés négatifs. Ces résultats sur l´absence de cas sévère, le taux élevé de guérison et la négativité des tests chez les personnes en contact étroit avec les malades pourraient s´expliquer par un portage de coronavirus non viable ou à charge virale très faible (non détectable). En effet, certains facteurs tels que le climat, les prédispositions génétiques pourraient jouer un rôle très important sur la viabilité de SARS CoV-2. Les autres virus respiratoires tels qu´Influenza virus, VRS, rhinovirus, entérovirus, métapneumovirus, para influenza virus causant les mêmes symptômes que le SARS CoV-2, leur détection devrait être faite ensemble pour l´imputabilité de la maladie à un tel virus respiratoire. En conclusion, au Sénégal, le nombre de personnes supposées malades de COVID-19 est très faible et le taux de guérison très élevé. Ainsi, les efforts déployés contre le COVID-19 devraient être réorientés vers la prise en charge des autres pathologies prioritaires des sénégalais.

Influenza surveillance during the 2009-2010, 2010-2011, 2011-2012, and 2012-2013 seasons in Algeria

We report the activity and circulation of influenza viruses in Algeria during four influenza seasons, from a national surveillance study carried out from 2009-2010 to 2012-2013. A total of 2766 samples from in- and outpatients, with no age restriction, were collected. The overall proportion of specimens that tested influenza positive was 46.0%. Overall, 96.6% of influenza A viruses were subtyped, and A/H1 subtypes accounted for 57.3% of influenza A viruses. Influenza A/H1 and A/H3 virus subtypes cocirculated in 2009-2010. In 2010-2011, a high proportion of type B viruses (66.2%) was observed. The subtype H3N2 was identified in 99% of cases typed in 2011-2012. Influenza A/H3N2 and B virus cocirculated in 2012-2013. A remarkably low influenza vaccination rate of 2.4% was observed among all age groups. Antibiotics were prescribed for 926 (41.3%) patients, and no difference was observed between patients with confirmed influenza and patients with influenza-like illness not related to influenza. The burden of influenza is largely undocumented in Algeria and strategies to expand this surveillance across the country are needed. Strategies to increase vaccination coverage are warranted to control and prevent influenza in individuals at risk of complications as well as in the general population.

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.

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.

Understanding user requirements to improve adoption of influenza diagnostics in clinical care within Metro Manila

BACKGROUND AND AIM

Influenza diagnostics play a critical role informing in clinical management decisions and defining the global epidemiology of the disease to support public health responses. Use of influenza diagnostics within most low-income and middle-income countries remains limited, including in the Philippines, where they are currently used only for epidemiologic surveillance. The aim of this study was to define key considerations, including product characteristics, which may influence future adoption, uptake, and integration of influenza diagnostics into public and private clinical settings in this emerging Asian market.

METHODS

Our study was conducted using a convenience sample of public and private hospital laboratories in Metro Manila. A usability assessment was conducted that included interviews with decision-makers and direct observation of laboratory end users using 2 platforms representative of emerging diagnostic products: (1) a point-of-care antigen-based rapid immunoassay diagnostic test paired with a reader and (2) a molecular diagnostic platform intended for decentralized use. Data were analyzed to assess user errors and device failure modes with each platform and to determine key considerations related to product adoption and uptake.

RESULTS

The most difficult test step for most users on both platforms involved sample preparation. When deciding to adopt a new test, priority product attributes include performance, potential volume of demand from clinicians, equipment cost, and ease of use. Demand for new tests is likely going to be driven by clinicians, and policies and guidelines will be needed to support the introduction of new products.

CONCLUSION

Adoption of influenza diagnostics in Metro Manila is feasible but will require affordable products capable of satisfying needs for use in both epidemiologic surveillance and clinical management.

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.

Pandemic Influenza: A Comparative Ethical Approach

Community-networks such as families and schools may foster and propagate some types of public health disasters. For such disasters, a communitarian-oriented ethical lens offers useful perspectives into the underlying relational nexus that favors the spread of infection. This chapter compares two traditional bioethical lenses—the communitarian and care ethics framework—vis-à-vis their capacities to engage the moral quandaries elicited by pandemic influenza. It argues that these quandaries preclude the analytical lens of ethical prisms that are individual-oriented but warrant a people-oriented approach. Adopting this dual approach offers both a contrastive and a complementary way of rethinking the underlying socioethical tensions elicited by pandemic influenza in particular and other public health disasters generally.

Induction of a robust immune response against avian influenza virus following transdermal inoculation with H5-DNA vaccine formulated in modified dendrimer-based delivery system in mouse model

This study was aimed to evaluate the immunogenicity of recombinant plasmid deoxyribonucleic acid (DNA), pBud-H5-green fluorescent protein (GFP)-interferon-regulatory factor (IRF)3 following delivery using polyamidoamine (PAMAM) dendrimer and transactivator of transcription (TAT)-conjugated PAMAM dendrimer as well as the effect of IRF3 as the genetic adjuvant. BALB/c mice were vaccinated transdermally with pBud-H5-GFP, PAMAM/pBud-H5-GFP, TAT-PAMAM/pBud-H5-GFP, and TAT-PAMAM/pBud-H5-GFP-IRF3. The expression analysis of H5 gene from the blood by using quantitative real-time reverse transcriptase polymerase chain reaction confirmed the ability of PAMAM dendrimer as a carrier for gene delivery, as well as the ability of TAT peptide to enhance the delivery efficiency of PAMAM dendrimer. Mice immunized with modified PAMAM by TAT peptide showed higher hemagglutination inhibition titer, and larger CD3⁺/CD4⁺ T cells and CD3⁺/CD8⁺ T cells population, as well as the production of cytokines, namely, interferon (IFN)-γ, interleukin (IL)-2, IL-15, IL-12, IL-6, and tumor necrosis factor-α compared with those immunized with native PAMAM. These results suggest that the function of TAT peptide as a cell-penetrating peptide is able to enhance the gene delivery, which results in rapid distribution of H5 in the tissues of the immunized mice. Furthermore, pBud-H5-GFP co-expressing IRF3 as a genetic adjuvant demonstrated the highest hemagglutination inhibition titer besides larger CD3⁺/CD4⁺ and CD3⁺/CD8⁺ T cells population, and strong Th1-like cytokine responses among all the systems tested. In conclusion, TAT-PAMAM dendrimer-based delivery system with IRF3 as a genetic adjuvant is an attractive transdermal DNA vaccine delivery system utilized to evaluate the efficacy of the developed DNA vaccine in inducing protection during challenge with virulent H5N1 virus.

[Literature review on human influenza epidemics occurred before the implementation plan for sentinel surveillance program in the DRC]

In the Democratic Republic of the Congo (DRC), several influenza epidemics are ignored because they are confused with other infectious diseases which have similar symptoms. Our study aims to assess influenza epidemics occurred in the DRC before 2008, year of the implementation of the influenza surveillance program in the DRC. We searched all the documents [articles, report,…] about influenza epidemic or acute respiratory infections [ARI] in the DRC before 2008 by using chosen key words. Epidemic description elements were identified and analyzed in each report. 4 documents have been found that had no article published. The sites of the epidemic outbreak were the rural health zones in Koshibanda and Kahemba, Bandundu [1995 and 2007], in Bosobolo, Equator [2002] and in Kinshasa [2002-2003]. Attack and lethality rates were 3.9% and 16% in Koshibanda respectively; 0.1% and 2% in Kinshasa; 47.5% and 1.5% in Bosobolo and 14.6% and 2.9% in Kahemba. Children less than 5 years of age were the most affected. Their attack rates ranged between 22.6 and 57.7% and lethality rates ranged between 3.2 and 3.7%. The two epidemics in Bosobolo and Kinshasa were associated with H3N2 influenza virus. This literature review highlights a high morbidity and mortality due to rare influenza epidemics in the DRC.

Sentinel surveillance for influenza among severe acute respiratory infection and acute febrile illness inpatients at three hospitals in Ghana

Background

Influenza epidemiology in Africa is generally not well understood. Using syndrome definitions to screen patients for laboratory confirmation of infection is an established means to effectively conduct influenza surveillance.

Methods

To compare influenza‐related epidemiologic data, from October 2010 through March 2013, we enrolled hospitalized severe acute respiratory infection (SARI; fever with respiratory symptoms) and acute febrile illness (AFI; fever without respiratory or other localizing symptoms) patients from three referral hospitals in Ghana. Demographic and epidemiologic data were obtained from enrolled patients after which nasopharyngeal and oropharyngeal swabs were collected, and processed by molecular methods for the presence of influenza viruses.

Results

Of 730 SARI patients, 59 (8%) were influenza positive; of 543 AFI patients, 34 (6%) were positive for influenza. Both SARI and AFI surveillance yielded influenza A(H3N2) (3% versus 1%), A(H1N1)pdm09 (2% versus 1%), and influenza B (3% versus 4%) in similar proportions. Data from both syndromes show year‐round influenza transmission but with increased caseloads associated with the rainy seasons.

Conclusions

As an appreciable percentage of influenza cases (37%) presented without defined respiratory symptoms, and thus met the AFI but not the SARI definition, it is important to consider broader screening criteria (i.e., AFI) to identify all laboratory‐confirmed influenza. The identified influenza transmission seasonality has important implications for the timing of related public health interventions.

Which influenza vaccine formulation should be used in Kenya? A comparison of influenza isolates from Kenya to vaccine strains, 2007-2013

INTRODUCTION

Every year the World Health Organization (WHO) recommends which influenza virus strains should be included in a northern hemisphere (NH) and a southern hemisphere (SH) influenza vaccine. To determine the best vaccine formulation for Kenya, we compared influenza viruses collected in Kenya from April 2007 to May 2013 to WHO vaccine strains.

METHODS

We collected nasopharyngeal and oropharyngeal (NP/OP) specimens from patients with respiratory illness, tested them for influenza, isolated influenza viruses from a proportion of positive specimens, tested the isolates for antigenic relatedness to vaccine strains, and determined the percentage match between circulating viruses and SH or NH influenza vaccine composition and schedule.

RESULTS

During the six years, 7.336 of the 60,072 (12.2%) NP/OP specimens we collected were positive for influenza: 30,167 specimens were collected during the SH seasons and 3717 (12.3%) were positive for influenza; 2903 (78.1%) influenza A, 902 (24.2%) influenza B, and 88 (2.4%) influenza A and B positive specimens. We collected 30,131 specimens during the NH seasons and 3978 (13.2%) were positive for influenza; 3181 (80.0%) influenza A, 851 (21.4%) influenza B, and 54 (1.4%) influenza A and B positive specimens. Overall, 362/460 (78.7%) isolates from the SH seasons and 316/338 (93.5%) isolates from the NH seasons were matched to the SH and the NH vaccine strains, respectively (p<0.001). Overall, 53.6% and 46.4% SH and NH vaccines, respectively, matched circulating strains in terms of vaccine strains and timing.

CONCLUSION

In six years of surveillance in Kenya, influenza circulated at nearly equal levels during the SH and the NH influenza seasons. Circulating viruses were matched to vaccine strains. The vaccine match decreased when both vaccine strains and timing were taken into consideration. Either vaccine formulation could be suitable for use in Kenya but the optimal timing for influenza vaccination needs to be determined.

Uptake and Effectiveness of a Trivalent Inactivated Influenza Vaccine in Children in Urban and Rural Kenya, 2010 to 2012

BACKGROUND

In Africa, recent surveillance has demonstrated a high burden of influenza, but influenza vaccine is rarely used. In Kenya, a country with a tropical climate, influenza has been shown to circulate year-round, like in other tropical countries.

METHODS

During 3 months in 2010 and 2011 and 2 months in 2012, the Kenya Medical Research Institute/Centers for Disease Control and Prevention-Kenya offered free injectable trivalent inactivated influenza vaccine to children 6 months to 10 years old in 2 resource-poor communities in Kenya-Kibera and Lwak (total population ~50,000). We conducted a case-control study to evaluate vaccine effectiveness (VE) in preventing laboratory-confirmed influenza associated with influenza-like illness and acute lower respiratory illness.

RESULTS

Of the approximately 18,000 eligible children, 41%, 48% and 51% received at least 1 vaccine in 2010, 2011 and 2012, respectively; 30%, 36% and 38% were fully vaccinated. VE among fully vaccinated children was 57% [95% confidence interval (CI): 29% to 74%] during a 6-month follow-up period, 39% (95% CI: 17% to 56%) during a 9-month follow-up period and 48% (95% CI: 32% to 61%) during a 12-month follow-up period. For the 12-month follow-up period, VE was statistically significant in children <5 years and in children 5 to <10 years old (50% and 46%, respectively).

CONCLUSIONS

In Kenya, parents of nearly half of the eligible children <10 years old chose to get their children vaccinated with a free influenza vaccine. During a 12-month follow-up period, the vaccine was moderately effective in preventing medically attended influenza-associated respiratory illness.

Acute Febrile Illness and Influenza Disease Burden in a Rural Cohort Dedicated to Malaria in Senegal, 2012-2013

Background

African populations are considered to be particularly vulnerable to fever illnesses, including malaria, and acute respiratory disease, owing to limited resources and overcrowding. However, the overall burden of influenza in this context is poorly defined and incidence data for African countries are scarce. We therefore studied the fever syndrome incidence and more specifically influenza incidence in a cohort of inhabitants of Dielmo and Ndiop in Sokone district, Senegal.

Methods

Daily febrile-illness data were prospectively obtained from January 2012 to December 2013 from the cohort of the villages of Dielmo and Ndiop, initially dedicated to the study of malaria. Nasopharyngeal swabs were collected from, and malaria diagnosis tests (thick blood smears) carried out on, every febrile individual during clinical visits; reverse transcriptase-polymerase chain reaction was used to identify influenza viruses in the samples. Binomial negative regression analysis was used to study the relationship between the monthly incidence rate and various covariates.

Results

In Dielmo and Ndiop, the incidence of malaria has decreased, but fever syndromes remain frequent. Among the 1036 inhabitants included in the cohort, a total of 1,129 episodes of fever were reported. Influenza was present all year round with peaks in October-December 2012 and August 2013. The fever, ILI and influenza incidence density rates differed significantly between age groups. At both sites, the adjusted incidence relative risks for fever syndromes and ILI were significantly higher in the [6–24 months) than other age groups: 7.3 (95%CI: [5.7–9.3]) and 16.1 (95%CI: [11.1–23.3]) respectively. The adjusted incidence relative risk for influenza was significantly higher for the [0–6 months) than other age groups: 9.9 (95%CI: [2.9–33.6]). At both sites, incidence density rates were lowest among adults > = 50 years.

Conclusions

In this rural setting in Senegal, influenza was most frequent among the youngest children. Preventive strategies targeting this population should be implemented.

Potential Impact of Co-Infections and Co-Morbidities Prevalent in Africa on Influenza Severity and Frequency: A Systematic Review

Infectious diseases and underlying medical conditions common to Africa may affect influenza frequency and severity. We conducted a systematic review of published studies on influenza and the following co-infections or co-morbidities that are prevalent in Africa: dengue, malaria, measles, meningococcus, Pneumocystis jirovecii pneumonia (PCP), hemoglobinopathies, and malnutrition. Articles were identified except for influenza and PCP. Very few studies were from Africa. Sickle cell disease, dengue, and measles co-infection were found to increase the severity of influenza disease, though this is based on few studies of dengue and measles and the measles study was of low quality. The frequency of influenza was increased among patients with sickle cell disease. Influenza infection increased the frequency of meningococcal disease. Studies on malaria and malnutrition found mixed results. Age-adjusted morbidity and mortality from influenza may be more common in Africa because infections and diseases common in the region lead to more severe outcomes and increase the influenza burden. However, gaps exist in our knowledge about these interactions.

Etiology of pediatric fever in western Kenya: a case-control study of falciparum malaria, respiratory viruses, and streptococcal pharyngitis

In Kenya, more than 10 million episodes of acute febrile illness are treated annually among children under 5 years. Most are clinically managed as malaria without parasitological confirmation. There is an unmet need to describe pathogen-specific etiologies of fever. We enrolled 370 febrile children and 184 healthy controls. We report demographic and clinical characteristics of patients with Plasmodium falciparum, group A streptococcal (GAS) pharyngitis, and respiratory viruses (influenza A and B, respiratory syncytial virus [RSV], parainfluenza [PIV] types 1-3, adenovirus, human metapneumovirus [hMPV]), as well as those with undifferentiated fever. Of febrile children, 79.7% were treated for malaria. However, P. falciparum was detected infrequently in both cases and controls (14/268 [5.2%] versus 3/133 [2.3%], P = 0.165), whereas 41% (117/282) of febrile children had a respiratory viral infection, compared with 24.8% (29/117) of controls (P = 0.002). Only 9/515 (1.7%) children had streptococcal infection. Of febrile children, 22/269 (8.2%) were infected with > 1 pathogen, and 102/275 (37.1%) had fevers of unknown etiology. Respiratory viruses were common in both groups, but only influenza or parainfluenza was more likely to be associated with symptomatic disease (attributable fraction [AF] 67.5% and 59%, respectively). Malaria was overdiagnosed and overtreated. Few children presented to the hospital with GAS pharyngitis. An enhanced understanding of carriage of common pathogens, improved diagnostic capacity, and better-informed clinical algorithms for febrile illness are needed.

Comparison of a new transport medium with universal transport medium at a tropical field site

Limited data are available in rural Honduran settings describing the etiology of respiratory infections, partially due to limited specimen transport. A new molecular transport media (MTM) preserves released nucleic acid at ambient temperature for later detection. Prospective surveillance was conducted in a Honduran clinic to identify 233 children less than 5 years of age presenting with respiratory symptoms. We obtained 2 nasopharyngeal samples and stored 1 in PrimeStore® MTM at room temperature and 1 in universal transport media (UTM) at -80 °C. The specimens were then transported to Cincinnati Children's Hospital and tested for 16 respiratory viruses using a multiplex PCR panel. The 2 specimen collection systems were similar for detecting the 4 most common viruses: influenza (Kappa = 0.7676, P < 0.0001), human metapneumovirus (Kappa = 0.8770, P < 0.0001), respiratory syncytial virus (Kappa = 0.6849, P < 0.0001), and parainfluenza (Kappa = 0.8796, P < 0.0001). These results suggest that clinical specimens transported via PrimeStore® MTM and UTM yield similar viral multiplex PCR results.

Influenza-like illnesses in Senegal: not only focus on influenza viruses

Influenza surveillance in African countries was initially restricted to the identification of circulating strains. In Senegal, the network has recently been enhanced (i) to include epidemiological data from Dakar and other regions and (ii) to extend virological surveillance to other respiratory viruses. Epidemiological data from the sentinel sites is transmitted daily by mobile phone. The data include those for other febrile syndromes similar to influenza-like illnesses (ILI), corresponding to integrated approach. Also, clinical samples are randomly selected and analyzed for influenza and other respiratory viruses. There were 101,640 declared visits to the 11 sentinel sites between week 11-2012 and week 35-2013; 22% of the visits were for fever syndromes and 23% of the cases of fever syndrome were ILI. Influenza viruses were the second most frequent cause of ILI (20%), after adenoviruses (21%) and before rhinoviruses (18%) and enteroviruses (15%). Co-circulation and co-infection were frequent and were responsible for ILI peaks. The first months of implementation of the enhanced surveillance system confirmed that viruses other the influenza make large contributions to influenza-like illnesses. It is therefore important to consider these etiologies in the development of strategies to reduce respiratory infections. More informative tools and research studies are required to assess the burden of respiratory infections in developing countries.

Demographic, socio-economic and geographic determinants of seasonal influenza vaccine uptake in rural western Kenya, 2011

Influenza-associated acute lower respiratory infections cause a considerable burden of disease in rural and urban sub-Saharan Africa communities with the greatest burden among children. Currently, vaccination is the best way to prevent influenza infection and accompanying morbidities. We examined geographic, socio-economic and demographic factors that contributed to acceptance of childhood seasonal influenza vaccination among children living in a population-based morbidity surveillance system in rural western Kenya, where influenza vaccine was offered free-of-charge to children 6 months-10 years old from April to June, 2011. We evaluated associations between maternal and household demographic variables, socio-economic status, and distance from home to vaccination clinics with family vaccination status. 7249 children from 3735 households were eligible for vaccination. Of these, 2675 (36.9%) were fully vaccinated, 506 (7.0%) were partially vaccinated and 4068 (56.1%) were not vaccinated. Children living in households located >5km radius from the vaccination facilities were significantly less likely to be vaccinated (aOR=0.70; 95% CI 0.54-0.91; p=0.007). Children with mothers aged 25-34 and 35-44 years were more likely to be vaccinated than children with mothers less than 25 years of age (aOR=1.36; 95% CI 1.15-1.62; p<0.001; and aOR=1.35; 95% CI 1.10-1.64; p=0.003, respectively). Finally, children aged 2-5 years and >5 years of age (aOR=1.38; 95% CI 1.20-1.59; p<0.001; and aOR=1.41; 95% CI 1.23-1.63; p<0.001, respectively) and who had a sibling hospitalized within the past year (aOR=1.73; 95% CI 1.40-2.14; p<0.001) were more likely to be vaccinated. Shorter distance from the vaccination center, older maternal and child age, household administrator's occupation that did not require them to be away from the home, and having a sibling hospitalized during the past year were associated with increased likelihood of vaccination against influenza in western Kenya. These findings should inform the design of future childhood seasonal influenza vaccination campaigns in rural Kenya, and perhaps elsewhere in Africa.

Multiyear persistence of 2 pandemic A/H1N1 influenza virus lineages in West Africa

Our understanding of the global ecology of influenza viruses is impeded by historically low levels of viral surveillance in Africa. Increased genetic sequencing of African A/H1N1 pandemic influenza viruses during 2009–2013 revealed multiyear persistence of 2 viral lineages within West Africa, raising questions about the roles of reduced air traffic and the asynchrony of seasonal influenza epidemics among West African countries in the evolution of independent lineages. The potential for novel influenza virus lineages to evolve within Africa warrants intensified influenza surveillance in Africa and other understudied areas.

Virological Surveillance of Influenza Viruses during the 2008-09, 2009-10 and 2010-11 Seasons in Tunisia

Background

The data contribute to a better understanding of the circulation of influenza viruses especially in North-Africa.

Objective

The objective of this surveillance was to detect severe influenza cases, identify their epidemiological and virological characteristics and assess their impact on the healthcare system.

Method

We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses' infection during three seasons in Tunisia.

Results

The 2008–09 winter influenza season is underway in Tunisia, with co-circulation of influenza A/H3N2 (56.25%), influenza A(H1N1) (32.5%), and a few sporadic influenza B viruses (11.25%). In 2010–11 season the circulating strains are predominantly the 2009 pandemic influenza A(H1N1)pdm09 (70%) and influenza B viruses (22%). And sporadic viruses were sub-typed as A/H3N2 and unsubtyped influenza A, 5% and 3%, respectively. Unlike other countries, highest prevalence of influenza B virus Yamagata-like lineage has been reported in Tunisia (76%) localised into the clade B/Bangladesh/3333/2007. In the pandemic year, influenza A(H1N1)pdm09 predominated over other influenza viruses (95%). Amino acid changes D222G and D222E were detected in the HA gene of A(H1N1)pdm09 virus in two severe cases, one fatal case and one mild case out of 50 influenza A(H1N1)pdm09 viruses studied. The most frequently reported respiratory virus other than influenza in three seasons was RSV (45.29%).

Conclusion

This article summarises the surveillance and epidemiology of influenza viruses and other respiratory viruses, showing how rapid improvements in influenza surveillance were feasible by connecting the existing structure in the health care system for patient records to electronic surveillance system for reporting ILI cases.

Swine influenza in sub-saharan Africa--current knowledge and emerging insights

Pigs have been associated with several episodes of influenza outbreaks in the past and are considered to play a significant role in the ecology of influenza virus. The recent 2009 pandemic influenza A/H1N1 virus originated from swine and not only did it cause widespread infection in humans, but was also transmitted back to swine in Asia, Europe and America. What may be the prevailing situation in Africa, particularly in sub-Saharan Africa, with respect to the circulation of classical swine or pandemic influenza? The ecology of influenza viruses, as well as the epidemiology of human or animal influenza, is poorly understood in the region. In particular, little is known about swine influenza in Africa despite the relevance of this production in the continent and the widespread pig husbandry operations in urban and rural areas. In this review, the gap in the knowledge of classical and pandemic swine influenza is attributed to negligence of disease surveillance, as well as to the economic and public health impact that the disease may cause in sub-Saharan Africa. However, emerging serological and virological evidence of swine influenza virus in some countries in the region underscores the importance of integrated surveillance to better understand the circulation and epidemiology of swine influenza, a disease of global economic and public health importance.

Overview of influenza virus infections in Kenya: past, present and future

The World Health Organization (WHO) estimates that acute lower respiratory infections account for 4 million deaths per year. The rates are even higher in developing countries. Influenza, a virus causing respiratory infections, has widely been studied in developed countries. However, there is paucity of data on its epidemiology, seasonality and burden in most developing countries. In the contrary, Kenya (a developing country) has an elaborate national epidemio-surveillance network for influenza, where a lot of data is generated on the epidemiology and seasonality of influenza in Kenya and the East African region. Several steps have been taken to control influenza in Kenya, including vaccination and surveillance programs. However, some challenges still exist. This article explores the pattern of influenza and existing interventions in Kenya, and highlights suggestions on what can be done to adequately control this virus in future.

Estimation of the national disease burden of influenza-associated severe acute respiratory illness in Kenya and Guatemala: a novel methodology

Background

Knowing the national disease burden of severe influenza in low-income countries can inform policy decisions around influenza treatment and prevention. We present a novel methodology using locally generated data for estimating this burden.

Methods and Findings

This method begins with calculating the hospitalized severe acute respiratory illness (SARI) incidence for children <5 years old and persons ≥5 years old from population-based surveillance in one province. This base rate of SARI is then adjusted for each province based on the prevalence of risk factors and healthcare-seeking behavior. The percentage of SARI with influenza virus detected is determined from provincial-level sentinel surveillance and applied to the adjusted provincial rates of hospitalized SARI. Healthcare-seeking data from healthcare utilization surveys is used to estimate non-hospitalized influenza-associated SARI. Rates of hospitalized and non-hospitalized influenza-associated SARI are applied to census data to calculate the national number of cases. The method was field-tested in Kenya, and validated in Guatemala, using data from August 2009–July 2011. In Kenya (2009 population 38.6 million persons), the annual number of hospitalized influenza-associated SARI cases ranged from 17,129–27,659 for children <5 years old (2.9–4.7 per 1,000 persons) and 6,882–7,836 for persons ≥5 years old (0.21–0.24 per 1,000 persons), depending on year and base rate used. In Guatemala (2011 population 14.7 million persons), the annual number of hospitalized cases of influenza-associated pneumonia ranged from 1,065–2,259 (0.5–1.0 per 1,000 persons) among children <5 years old and 779–2,252 cases (0.1–0.2 per 1,000 persons) for persons ≥5 years old, depending on year and base rate used. In both countries, the number of non-hospitalized influenza-associated cases was several-fold higher than the hospitalized cases.

Conclusions

Influenza virus was associated with a substantial amount of severe disease in Kenya and Guatemala. This method can be performed in most low and lower-middle income countries.

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.

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.

Sentinel surveillance for influenza in Senegal, 1996-2009

BACKGROUND

Data on influenza in tropical and resource-limited countries are scarce. In this study we present results from 14 years of influenza surveillance in Senegal, one of the few tropical countries in Africa from which longitudinal data are available.

METHODS

From 1996 to 2009, we collected respiratory specimens from outpatients presenting with influenza-like illness at 13 facilities in order to investigate the epidemiology of seasonal influenza and the characteristics of the circulating influenza viruses. Specimens were tested for influenza using viral isolation and/or reverse-transcription polymerase chain reaction (RT-PCR).

RESULTS

From 1996 to 2009, specimens were obtained from 9176 patients; 1233 (13%) were influenza-positive by virus isolation and/or RT-PCR. Among positive samples, 958 (77%) were influenza A, 268 (22%) influenza B, and 7 (1%) influenza type C; of influenza A viruses, 619 (65%) were A(H3) and 339 (35%) A(H1), of which 13 (1%) were identified as H1N2. The proportion positive was similar for children <15 years, young adults 16-35 years, and adults 36-55 years (15%), but lower for persons >55 years (9%). Although influenza A(H1), A(H3), and B all circulated during most years, influenza A(H3N2) predominated during 9 of the 14 years. Influenza activity consistently peaked during the rainy season (July-September). Phylogenetic analysis showed that viruses circulating in Senegal were similar to contemporary viruses circulating elsewhere in the world.

CONCLUSIONS

Our data confirm that influenza is prevalent in Senegal, occurs in seasonal epidemics, and contributes to the burden of respiratory diseases in all age groups.

Sentinel surveillance for influenza-like illness, severe acute respiratory illness, and laboratory-confirmed influenza in Kinshasa, Democratic Republic of Congo, 2009-2011

Little is known about influenza in central Africa. We conducted sentinel surveillance for influenza-like illness, severe acute respiratory illness, and laboratory-confirmed influenza at 5 sites in Kinshasa, Democratic Republic of Congo, from January 2009 through April 2011. We obtained samples from 4156 patients, of whom 605 (15%) had specimens containing laboratory-confirmed influenza virus. Apart from the period of pandemic influenza due to influenza A virus subtype H1N1, which occurred during August-December 2009, influenza activity peaked at least once each year from January through March, predominantly among children. These data can guide interventions to reduce the burden of influenza in the Democratic Republic of Congo and central Africa.

Influenza viruses in Nigeria, 2009-2010: results from the first 17 months of a national influenza sentinel surveillance system

BACKGROUND

Influenza surveillance data from tropical, sub-Saharan African countries are limited. To better understand the epidemiology of influenza, Nigeria initiated influenza surveillance in 2008.

METHODS

Outpatients with influenza-like illness (ILI) and inpatients with severe acute respiratory illness (SARI) were enrolled at 4 sentinel facilities. Epidemiologic data were obtained, and respiratory specimens were tested for influenza viruses, using real-time reverse-transcription polymerase chain reaction assays.

RESULTS

During April 2009-August 2010, 2841 patients were enrolled. Of 2803 specimens tested, 217 (7.7%) were positive for influenza viruses (167 [8%] were from subjects with ILI, 17 [5%] were from subjects with SARI, and 33 were from subjects with an unclassified condition). During the prepandemic period, subtype H3N2 (A[H3N2]) was the dominant circulating influenza A virus subtype; 2009 pandemic influenza A virus subtype H1N1 (A[H1N1]pdm09) replaced A(H3N2) as the dominant circulating virus during November 2009. Among persons with ILI, A(H1N1)pdm09 was most frequently found in children aged 5-17 years, whereas among subjects with SARI, it was most frequently found in persons aged ≥ 65 years. The percentage of specimens that tested positive for influenza viruses peaked at 18.9% in February 2010, and the majority were A(H1N1)pdm09.

CONCLUSIONS

Influenza viruses cause ILI and SARI in Nigeria. Data from additional years are needed to better understand the epidemiology and seasonality of influenza viruses in Nigeria.

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.

Etiology and seasonality of viral respiratory infections in rural Honduran children

BACKGROUND

Limited data are available in Honduras that describe the etiology and seasonality of respiratory infections, especially in rural outpatient settings. Better data may lead to improved therapeutic and preventive strategies. The goal of our study was to determine the viral etiology and seasonality of acute respiratory infections in a rural Honduran population of children.

METHODS

Prospective clinic surveillance was conducted to identify children < 5 years of age presenting with respiratory symptoms of < 5 days duration. We obtained data on age, sex, medical history, breastfeeding history, symptoms, risk factors, household setting, temperature, respiratory rate and chest examination findings. To assess the association between specific viruses and weather, regional meteorological data were collected. Nasopharyngeal samples were tested for 16 respiratory viruses using a multiplex polymerase chain reaction panel.

RESULTS

From February 2010 through June 2011, 345 children < 5 years of age were enrolled; 17%, 23%, 30% and 31% were <6, 6-11, 12-23 and 24-60 months old, respectively. Including all clinics in the region, 44.5% of patients < 5 years of age with documented respiratory diagnoses were enrolled. At least 1 virus was identified in 75.4% children, of which 7.5% were coinfections; 13.3% were positive for parainfluenza, 11.9% for influenza, 8.1% for human metapneumovirus and 7.5% for respiratory syncytial virus. Rainfall correlated with parainfluenza (P < 0.0001), influenza (P < 0.0001), human metapneumovirus (P = 0.0182) and respiratory syncytial virus (P < 0.0001).

CONCLUSIONS

These results suggest that the spectrum of viruses in ill, rural, Honduran children is similar to that in North and Central America, although the seasonality is typical of some tropical regions.

Influenza and malaria coinfection among young children in western Kenya, 2009-2011

BACKGROUND

Although children <5 years old in sub-Saharan Africa are vulnerable to both malaria and influenza, little is known about coinfection.

METHODS

This retrospective, cross-sectional study in rural western Kenya examined outpatient visits and hospitalizations associated with febrile acute respiratory illness (ARI) during a 2-year period (July 2009-June 2011) in children <5 years old.

RESULTS

Across sites, 45% (149/331) of influenza-positive patients were coinfected with malaria, whereas only 6% (149/2408) of malaria-positive patients were coinfected with influenza. Depending on age, coinfection was present in 4%-8% of outpatient visits and 1%-3% of inpatient admissions for febrile ARI. Children with influenza were less likely than those without to have malaria (risk ratio [RR], 0.57-0.76 across sites and ages), and children with malaria were less likely than those without to have influenza (RR, 0.36-0.63). Among coinfected children aged 24-59 months, hospital length of stay was 2.7 and 2.8 days longer than influenza-only-infected children at the 2 sites, and 1.3 and 3.1 days longer than those with malaria only (all P < .01).

CONCLUSIONS

Coinfection with malaria and influenza was uncommon but associated with longer hospitalization than single infections among children 24-59 months of age.

Improving influenza surveillance in sub-Saharan Africa

PROBLEM

Little is known about the burden of influenza in sub-Saharan Africa. Routine influenza surveillance is key to getting a better understanding of the impact of acute respiratory infections on sub-Saharan African populations.

APPROACH

A project known as Strengthening Influenza Sentinel Surveillance in Africa (SISA) was launched in Angola, Cameroon, Ghana, Nigeria, Rwanda, Senegal, Sierra Leone and Zambia to help improve influenza sentinel surveillance, including both epidemiological and virological data collection, and to develop routine national, regional and international reporting mechanisms. These countries received technical support through remote supervision and onsite visits. Consultants worked closely with health ministries, the World Health Organization, national influenza laboratories and other stakeholders involved in influenza surveillance.

LOCAL SETTING

Influenza surveillance systems in the target countries were in different stages of development when SISA was launched. Senegal, for instance, had conducted virological surveillance for years, whereas Sierra Leone had no surveillance activity at all.

RELEVANT CHANGES

Working documents such as national surveillance protocols and procedures were developed or updated and training for sentinel site staff and data managers was organized.

LESSONS LEARNT

Targeted support to countries can help them strengthen national influenza surveillance, but long-term sustainability can only be achieved with external funding and strong national government leadership.

Excess mortality associated with the 2009 A(H1N1)v influenza pandemic in Antananarivo, Madagascar

It is difficult to assess the mortality burden of influenza epidemics in tropical countries. Until recently, the burden of influenza was believed to be negligible in Africa. We assessed the impact of the 2009 influenza epidemic on mortality in Madagascar by conducting Poisson regression analysis on mortality data from the deaths registry, after the first wave of the 2009 A(H1N1) virus pandemic. There were 20% more human deaths than expected in Antananarivo, Madagascar in November 2009, with excess mortality in the ⩾50 years age group (relative risk 1·41). Furthermore, the number of deaths from pulmonary disease was significantly higher than the number of deaths from other causes during this pandemic period. These results suggest that the A(H1N1) 2009 virus pandemic may have been accompanied by an increase in mortality.

Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: a modelling study

BACKGROUND

18,500 laboratory-confirmed deaths caused by the 2009 pandemic influenza A H1N1 were reported worldwide for the period April, 2009, to August, 2010. This number is likely to be only a fraction of the true number of the deaths associated with 2009 pandemic influenza A H1N1. We aimed to estimate the global number of deaths during the first 12 months of virus circulation in each country.

METHODS

We calculated crude respiratory mortality rates associated with the 2009 pandemic influenza A H1N1 strain by age (0-17 years, 18-64 years, and >64 years) using the cumulative (12 months) virus-associated symptomatic attack rates from 12 countries and symptomatic case fatality ratios (sCFR) from five high-income countries. To adjust crude mortality rates for differences between countries in risk of death from influenza, we developed a respiratory mortality multiplier equal to the ratio of the median lower respiratory tract infection mortality rate in each WHO region mortality stratum to the median in countries with very low mortality. We calculated cardiovascular disease mortality rates associated with 2009 pandemic influenza A H1N1 infection with the ratio of excess deaths from cardiovascular and respiratory diseases during the pandemic in five countries and multiplied these values by the crude respiratory disease mortality rate associated with the virus. Respiratory and cardiovascular mortality rates associated with 2009 pandemic influenza A H1N1 were multiplied by age to calculate the number of associated deaths.

FINDINGS

We estimate that globally there were 201,200 respiratory deaths (range 105,700-395,600) with an additional 83,300 cardiovascular deaths (46,000-179,900) associated with 2009 pandemic influenza A H1N1. 80% of the respiratory and cardiovascular deaths were in people younger than 65 years and 51% occurred in southeast Asia and Africa.

INTERPRETATION

Our estimate of respiratory and cardiovascular mortality associated with the 2009 pandemic influenza A H1N1 was 15 times higher than reported laboratory-confirmed deaths. Although no estimates of sCFRs were available from Africa and southeast Asia, a disproportionate number of estimated pandemic deaths might have occurred in these regions. Therefore, efforts to prevent influenza need to effectively target these regions in future pandemics.

FUNDING

None.

Willingness to receive pandemic influenza A (H1N1) vaccine among doctors and nurses in public health facilities in Ibadan, Nigeria

BACKGROUND

As part of global efforts to contain the spread of the 2009 pandemic influenza A (H1N1), the Federal Ministry of Health of Nigeria is embarking on the vaccination of health care workers employed in health facilities nationwide. This study was designed to assess the willingness of doctors and nurses working in public health facilities in Ibadan, Nigeria to receive the influenza A (H1N1) vaccine.

METHODS

A descriptive cross-sectional study design was employed. Stratified simple random sampling was used to select a total of 304 doctors and nurses who worked at the public primary (70), secondary (51) and tertiary (183) levels of health care facilities in Ibadan. A self-administered, structured questionnaire that contained items on socio-demographics, sources of information, knowledge about the infection and the vaccine, risk perception, willingness to receive the vaccine and suggestions to improve vaccination acceptance by health-care workers was used to collect the data.

MAIN FINDINGS

A total of 255 providers responded for an overall response rate of 84%. The mean age of the respondents was 35.0 ± 9.7 years. A high proportion (88.2%) of the participants, including 94.9% of the doctors and 87.0% of the nurses, reported a willingness to receive the vaccine. Perceptions regarding the risk of contracting influenza, the availability of effective vaccinations for prevention and beliefs that the disease is fatal were reasons given by respondents who reported willingness to receive the vaccination. Those participants who reported ever hearing about the pandemic (AOR 2.0, 95% CI 1.2-3.2) and those who had a high-risk perception of contracting the disease (AOR 2.0, 95% CI 1.2-3.7) were likely to receive the vaccine.

CONCLUSION

Doctors and nurses at the three levels of health care facilities in Ibadan were willing to receive the pandemic influenza A (H1N1) vaccine. Efforts should be made to deliver the vaccines via adequate planning.

Influenza transmission during a one-year period (2009-2010) in a Sahelian city: low temperature plays a major role

Please cite this paper as: Jusot J‐François et al. (2011) Influenza transmission during a one‐year period (2009–2010) in a Sahelian city: low temperature plays a major role. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750‐2659.2011.00286.x.

This work aimed at studying the link between some climatic factors and the occurrence of influenza in Niamey, Niger. Patients with influenza like illness or severe acute respiratory illness were recruited through a sentinel network. A nasopharyngeal swab was sampled and tested for influenza viruses A and B by RT‐PCR. Time series of daily counts of influenza cases and climatic factors were linked using a generalized additive model. Among the 320 patients recruited, 76 were confirmed positive for influenza. Influenza cases increased significantly with minimal temperatures and high visibility. This work brings some valuable explanation to the impact of low temperatures on influenza transmission.

Influenza surveillance among outpatients and inpatients in Morocco, 1996-2009

BACKGROUND

There is limited information about the epidemiology of influenza in Africa. We describe the epidemiology and seasonality of influenza in Morocco from 1996 to 2009 with particular emphasis on the 2007-2008 and 2008-2009 influenza seasons. Successes and challenges of the enhanced surveillance system introduced in 2007 are also discussed.

METHODS

Virologic sentinel surveillance for influenza virus was initiated in Morocco in 1996 using a network of private practitioners that collected oro-pharyngeal and naso-pharyngeal swabs from outpatients presenting with influenza-like-illness (ILI). The surveillance network expanded over the years to include inpatients presenting with severe acute respiratory illness (SARI) at hospitals and syndromic surveillance for ILI and acute respiratory infection (ARI). Respiratory samples and structured questionnaires were collected from eligible patients, and samples were tested by immunofluorescence assays and by viral isolation for influenza viruses.

RESULTS

We obtained a total of 6465 respiratory specimens during 1996 to 2009, of which, 3102 were collected during 2007-2009. Of those, 2249 (72%) were from patients with ILI, and 853 (27%) were from patients with SARI. Among the 3,102 patients, 98 (3%) had laboratory-confirmed influenza, of whom, 85 (87%) had ILI and 13 (13%) had SARI. Among ILI patients, the highest proportion of laboratory-confirmed influenza occurred in children less than 5 years of age (3/169; 2% during 2007-2008 and 23/271; 9% during 2008-2009) and patients 25-59 years of age (8/440; 2% during 2007-2009 and 21/483; 4% during 2008-2009). All SARI patients with influenza were less than 14 years of age. During all surveillance years, influenza virus circulation was seasonal with peak circulation during the winter months of October through April.

CONCLUSION

Influenza results in both mild and severe respiratory infections in Morocco, and accounted for a large proportion of all hospitalizations for severe respiratory illness among children 5 years of age and younger.

Transmission characteristics of the 2009 H1N1 influenza pandemic: comparison of 8 Southern hemisphere countries

While in Northern hemisphere countries, the pandemic H1N1 virus (H1N1pdm) was introduced outside of the typical influenza season, Southern hemisphere countries experienced a single wave of transmission during their 2009 winter season. This provides a unique opportunity to compare the spread of a single virus in different countries and study the factors influencing its transmission. Here, we estimate and compare transmission characteristics of H1N1pdm for eight Southern hemisphere countries/states: Argentina, Australia, Bolivia, Brazil, Chile, New Zealand, South Africa and Victoria (Australia). Weekly incidence of cases and age-distribution of cumulative cases were extracted from public reports of countries' surveillance systems. Estimates of the reproduction numbers, R₀, empirically derived from the country-epidemics' early exponential phase, were positively associated with the proportion of children in the populations (p = 0.004). To explore the role of demography in explaining differences in transmission intensity, we then fitted a dynamic age-structured model of influenza transmission to available incidence data for each country independently, and for all the countries simultaneously. Posterior median estimates of R₀ ranged 1.2–1.8 for the country-specific fits, and 1.29–1.47 for the global fits. Corresponding estimates for overall attack-rate were in the range 20–50%. All model fits indicated a significant decrease in susceptibility to infection with age. These results confirm the transmissibility of the 2009 H1N1 pandemic virus was relatively low compared with past pandemics. The pattern of age-dependent susceptibility found confirms that older populations had substantial – though partial - pre-existing immunity, presumably due to exposure to heterologous influenza strains. Our analysis indicates that between-country-differences in transmission were at least partly due to differences in population demography.

Although relatively mild, the 2009 H1N1 pandemic reminded us once again of the on-going threat posed by novel respiratory viruses and the need for understanding better how such pathogens emerge and spread. From April to September 2009, countries in temperate regions of the Southern hemisphere experienced large epidemics of H1N1pdm during their winter season, with the new virus quickly becoming the predominant circulating influenza strain. We use mathematical modelling to analyse H1N1pdm epidemiological data from 8 southern hemisphere countries. We aim at understanding better the factors which may have influenced virus transmission in these countries. We find that transmissibility of the virus was relatively low compared with previous influenza pandemics, largely because of strong pre-existing age-dependent susceptibility to the virus (older people being less susceptible to infection, perhaps due to pre-existing immunity). We suggest that population demography had a strong impact on the virus spread and that higher transmission rates occurred in countries having a younger population. Our results highlight the requirement to use age-structured models for the analysis of influenza epidemics and support the need for country-specific analyses to inform the design of control policies for pandemic mitigation.

Factors associated with death or intensive care unit admission due to pandemic 2009 influenza A (H1N1) infection

BACKGROUND

In preparation for pandemic HINI or H1N1 influenza (H1N1) it is necessary to identify factors associated with mortality of patients with HINI and hospital admissions to intensive care unit (ICU) of patients diagnosed in 2009 with HINI.

OBJECTIVES

To describe the clinical and epidemiological features associated with 2009 HIN1 mortality and ICU patient admissions to Masih Daneshvari Teaching Hospital, Iran.

METHODS

A retrospective cross-sectional study was conducted among patients with mortality and admissions to ICU with confirmed HINI. Demographic, clinical, laboratory, radiological findings, and epidemiologic data were abstracted from medical records, using a standardized datasheet.

RESULTS

From June through December 2009, 20 out of the 46 confirmed hospitalized patients with confirmed H1NI were admitted to the ICU and 7 (15%) died. Among various variables, opium inhalation (P = 0.01), having productive cough, hemoptysis, chest pain, confusion, and loss of consciousness were significantly related to ICU admission (P < 0.05). Pleural effusion (P = 0.006), elevated liver enzymes, as well as CPK and LDH level were significantly relevant to ICU admission (P < 0.05). Delayed antiviral treatment was more common among patients who died and the elderly.

DISCUSSION

Patients who were admitted to ICU with confirmed H1N1 included the following risk factors: delayed initiation of antiviral therapy, history of opium inhalation and symptoms including; productive cough, hemoptysis, chest pain, confusion, and loss of consciousness. The mortality rate in the study population was high but compares favorably with other recent published studies.