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Background: The first few 'X' (FFX) studies provide evidence to guide public health decision-making and resource allocation. The adapted WHO Unity FFX protocol for COVID-19 was implemented to gain an understanding of the clinical, epidemiological, virological and household transmission dynamics of the first cases of COVID-19 infection detected in Juba, South Sudan., Methods: Laboratory-confirmed COVID-19 cases were identified through the national surveillance system, and an initial visit was conducted with eligible cases to identify all close contacts. Consenting cases and close contacts were enrolled between June 2020 and December 2020. Demographic, clinical information and biological samples were taken at enrollment and 14-21 days post-enrollment for all participants., Results: Twenty-nine primary cases and 82 contacts were included in the analyses. Most primary cases (n = 23/29, 79.3%) and contacts (n = 61/82, 74.4%) were male. Many primary cases (n = 18/29, 62.1%) and contacts (n = 51/82, 62.2%) were seropositive for SARS-CoV-2 at baseline. The secondary attack rate among susceptible contacts was 12.9% (4/31; 95% CI: 4.9%-29.7%). All secondary cases and most (72%) primary cases were asymptomatic. Reported symptoms included coughing (n = 6/29, 20.7%), fever or history of fever (n = 4/29, 13.8%), headache (n = 3/29, 10.3%) and shortness of breath (n = 3/29, 10.3%). Of 38 cases, two were hospitalised (5.3%) and one died (2.6%)., Conclusions: These findings were used to develop the South Sudanese Ministry of Health surveillance and contract tracing protocols, informing local COVID-19 case definitions, follow-up protocols and data management systems. This investigation demonstrates that rapid FFX implementation is critical in understanding the emerging disease and informing response priorities., (© 2023 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.)

We aimed to estimate the household secondary infection attack rate (hSAR) of SARS-CoV-2 in investigations aligned with the WHO Unity Studies Household Transmission Investigations (HHTI) protocol. We conducted a systematic review and meta-analysis according to PRISMA 2020 guidelines. We searched Medline, Embase, Web of Science, Scopus and medRxiv/bioRxiv for "Unity-aligned" First Few X cases (FFX) and HHTIs published 1 December 2019 to 26 July 2021. Standardised early results were shared by WHO Unity Studies collaborators (to 1 October 2021). We used a bespoke tool to assess investigation methodological quality. Values for hSAR and 95% confidence intervals (CIs) were extracted or calculated from crude data. Heterogeneity was assessed by visually inspecting overlap of CIs on forest plots and quantified in meta-analyses. Of 9988 records retrieved, 80 articles (64 from databases; 16 provided by Unity Studies collaborators) were retained in the systematic review; 62 were included in the primary meta-analysis. hSAR point estimates ranged from 2% to 90% (95% prediction interval: 3%-71%; I 2  = 99.7%); I 2 values remained >99% in subgroup analyses, indicating high, unexplained heterogeneity and leading to a decision not to report pooled hSAR estimates. FFX and HHTI remain critical epidemiological tools for early and ongoing characterisation of novel infectious pathogens. The large, unexplained variance in hSAR estimates emphasises the need to further support standardisation in planning, conduct and analysis, and for clear and comprehensive reporting of FFX and HHTIs in time and place, to guide evidence-based pandemic preparedness and response efforts for SARS-CoV-2, influenza and future novel respiratory viruses., (© 2022 World Health Organization; licensed by John Wiley & Sons Ltd. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.)

During epidemic periods, HCW are vulnerable. In Africa, cohort studies implemented by the Institut Pasteur International Network in five countries showed after 3-month follow-up around 40% of the HCW have been infected by the SARS-CoV-2. So advocacy for HCW protection strategy need to be fostered and sustained by the health authorities all over the African continent., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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., (© 2020 Lagare A et al.)

Background: Respiratory syncytial virus (RSV)-associated acute lower respiratory infection is a common cause for hospitalization and hospital deaths in young children globally. There is urgent need to generate evidence to inform immunization policies when RSV vaccines become available. The WHO piloted a RSV surveillance strategy that leverages the existing capacities of the Global Influenza Surveillance and Response System (GISRS) to better understand RSV seasonality, high-risk groups, validate case definitions, and develop laboratory and surveillance standards for RSV., Methods: The RSV sentinel surveillance strategy was piloted in 14 countries. Patients across all age groups presenting to sentinel hospitals and clinics were screened all year-round using extended severe acute respiratory infection (SARI) and acute respiratory infection (ARI) case definitions for hospital and primary care settings, respectively. Respiratory specimens were tested for RSV at the National Influenza Centre (NIC) using standardized molecular diagnostics that had been validated by an External Quality Assurance program. The WHO FluMart data platform was adapted to receive case-based RSV data and visualize interactive visualization outputs., Results: Laboratory standards for detecting RSV by RT-PCR were developed. A review assessed the feasibility and the low incremental costs for RSV surveillance. Several challenges were addressed related to case definitions, sampling strategies, the need to focus surveillance on young children, and the data required for burden estimation., Conclusions: There was no evidence of any significant adverse impact on the functioning of GISRS which is primarily intended for virologic and epidemiological surveillance of influenza., (© 2019 The World Health Organization. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.)

Concerns have been expressed about the view point of WHO AFRO concerning research for health in the African Region. WHO AFRO considers research a critical component in the improvement of health in the Africa region. Ensuring the effectiveness of our strategies, policies and programmes requires evidence. In the context of the ongoing COVID-19 outbreak, WHO research interests cover key areas of the response. The WHO AFRO consider research as critical in our efforts at protecting people against health emergencies and pandemics like the COVID-19 and ensuring universal access to proven interventions. In view of this, the WHO has taken steps to strengthen capacity for research in the region. The results of these efforts may take time to manifest but will surely do as we persist in our drive, with support from our partners., Competing Interests: The authors declare no competing interests., (© Matshidiso Moeti et al.)

In 1998, the WHO African region adopted a strategy called Integrated Disease Surveillance and Response (IDSR). Here, we present the current status of IDSR implementation; and provide some future perspectives for enhancing the IDSR strategy in Africa. In 2017, we used two data sources to compile information on the status of IDSR implementation: a pretested rapid assessment questionnaire sent out biannually to all countries and quarterly compilation of data for two IDSR key performance indicators (KPI). The first KPI measures country IDSR performance and the second KPI tracks the number of countries that the WHO secretariat supports to scale up IDSR. The KPI data for 2017 were compared with a retrospective baseline for 2014. By December 2017, 44 of 47 African countries (94%) were implementing IDSR. Of the 44 countries implementing IDSR, 40 (85%) had initiated IDSR training at subnational level; 32 (68%) had commenced community-based surveillance; 35 (74%) had event-based surveillance; 33 (70%) had electronic IDSR; and 32 (68%) had a weekly/monthly bulletin for sharing IDSR data. Thirty-two countries (68%) had achieved the timeliness and completeness threshold of at least 80% of the reporting units. However, only 12 countries (26%) had the desired target of at least 90% IDSR implementation coverage at the peripheral level. After 20 years of implementing IDSR, there are major achievements in the indicator-based surveillance systems. However, major gaps were identified in event-based surveillance. All African countries should enhance IDSR everywhere., Competing Interests: Competing interests: None declared.

Introduction: in spite of the efforts and resources committed by the division of infectious disease and epidemiology (DIDE) of the national public health institute of Liberia (NPHIL)/Ministry of health to strengthening integrated disease surveillance and response (IDSR) across the country, quality data management system remains a challenge to the Liberia NPHIL/MoH (Ministry of health), with incomplete and inconsistent data constantly being reported at different levels of the surveillance system. As part of the monitoring and evaluation strategy for IDSR continuous improvement, data quality assessment (DQA) of the IDSR system to identify successes and gaps in the disease surveillance information system (DSIS) with the aim of ensuring data accuracy, reliability and credibility of generated data at all levels of the health system; and to inform an operational plan to address data quality needs for IDSR activities is required., Methods: multi-stage cluster sampling that included stage 1: simple random sample (SRS) of five counties, stage 2: simple random sample of two districts and stage 3: simple random sample of three health facilities was employed during the study pilot assessment done in Montserrado County with Liberia institute of bio medical research (LIBR) inclusive. A total of thirty (30) facilities was targeted, twenty nine (29) of the facilities were successfully audited: one hospital, two health centers, twenty clinics and respondents included: health facility surveillance focal persons (HFSFP), zonal surveillance officers (ZSOs), district surveillance officers (DSOs) and County surveillance officers (CSOs)., Results: the assessment revealed that data use is limited to risk communication and sensitization, no examples of use of data for prioritization or decision making at the subnational level. The findings indicated the following: 23% (7/29) of health facilities having dedicated phone for reporting, 20% (6/29) reported no cell phone network, 17% (5/29) reported daily access to internet, 56.6% (17/29) reported a consistent supply of electricity, and no facility reported access to functional laptop. It was also established that 40% of health facilities have experienced a stock out of laboratory specimens packaging supplies in the past year. About half of the surveyed health facilities delivered specimens through riders and were assisted by the DSOs. There was a large variety in the reported packaging process, with many staff unable to give clear processes. The findings during the exercise also indicated that 91% of health facility staff were mentored on data quality check and data management including the importance of the timeliness and completeness of reporting through supportive supervision and mentorship; 65% of the health facility assessed received supervision on IDSR core performance indicator; and 58% of the health facility officer in charge gave feedback to the community level., Conclusion: public health is a data-intensive field which needs high-quality data and authoritative information to support public health assessment, decision-making and to assure the health of communities. Data quality assessment is important for public health. In this review completeness, accuracy, and timeliness were the three most-assessed attributes. Quantitative data quality assessment primarily used descriptive surveys and data audits, while qualitative data quality assessment methods include primarily interviews, questionnaires administration, documentation reviews and field observations. We found that data-use and data-process have not been given adequate attention, although they were equally important factors which determine the quality of data. Other limitations of the previous studies were inconsistency in the definition of the attributes of data quality, failure to address data users' concerns and a lack of triangulation of mixed methods for data quality assessment. The reliability and validity of the data quality assessment were rarely reported. These gaps suggest that in the future, data quality assessment for public health needs to consider equally the three dimensions of data quality, data use and data process. Measuring the perceptions of end users or consumers towards data quality will enrich our understanding of data quality issues. Data use is limited to risk communication and sensitization, no examples of use of data for prioritization or decision making at the sub national level., Competing Interests: The authors declare no competing interest.

Introduction: Following a declaration by the World Health Organization that Liberia had successfully interrupted Ebola virus transmission on May 9th, 2015; the country entered a period of enhanced surveillance. The number of cases had significantly reduced prior to the declaration, leading to closure of eight out of eleven Ebola testing laboratories. Enhanced surveillance led to an abrupt increase in demand for laboratory services. We report interventions, achievements, lessons learned and recommendations drawn from enhancing laboratory capacity., Methods: Using archived data, we reported before and after interventions that aimed at increasing laboratory capacity. Laboratory capacity was defined by number of laboratories with Ebola Virus Disease (EVD) testing capacity, number of competent staff, number of specimens tested, specimen backlog, daily and surge testing capacity, and turnaround time. Using Stata 14 (Stata Corporation, College Station, TX, USA), medians and trends were reported for all continuous variables., Results: Between May and December 2015, interventions including recruitment and training of eight staff, establishment of one EVD laboratory facility, implementation of ten Ebola GeneXpert diagnostic platforms, and establishment of working shifts yielded an 8-fold increase in number of specimens tested, a reduction in specimens backlog to zero, and restoration of turn-around time to 24 hours. This enabled a more efficient surveillance system that facilitated timely detection and containment of two EVD clusters observed thereafter., Conclusion: Effective enhancement of laboratory services during high demand periods requires a combination of context-specific interventions. Building and ensuring sustainability of local capacity is an integral part of effective surveillance and disease outbreak response efforts., Competing Interests: The authors declare no competing interest.

Introduction: Early detection of disease outbreaks is paramount to averting associated morbidity and mortality. In January 2018, nine cases including four deaths associated with meningococcal disease were reported in three communities of Foya district, Lofa County, Liberia. Due to the porous borders between Lofa County and communities in neighboring Sierra Leone and Guinea, the possibility of epidemic spread of meningococcal disease could not be underestimated., Methods: The county incidence management system (IMS) was activated that coordinated the response activities. Daily meetings were conducted to review response activities progress and challenges. The district rapid response team (DRRT) was the frontline responders. The case based investigation form; case line list and contacts list were used for data collection. A data base was established and analysed daily for action. Tablets Ciprofloxacin were given for chemoprophylaxis., Results: Sixty-seven percent (67%) of the cases were males and also 67% of the affected age range was 3 to 14 years and attending primary school. The attack rate was 7/1,000 population and case fatality rate was 44.4 % with majority of the deaths occurring within 24-48 hours of symptoms onset. Three of the cases tested positive for Neisseria Meningitidis sero-type W while six cases were Epi-linked. None of the cases had recent meningococcal vaccination and no health-worker infections were registered., Conclusion: This cluster of cases of meningococcal disease during the meningitis season in a country that is not traditionally part of the meningitis belt emphasized the need for strengthening surveillance, preparedness and response capacity to meningitis., Competing Interests: The authors declare no competing interest.

Introduction: Measles is an acute viral disease that remains endemic in much of sub-Sahara Africa, including Liberia. The 2014 Ebola epidemic disrupted an already fragile health system contributing to low uptake of immunization services, population immunity remained low thus facilitating recurrent outbreaks of measles in Liberia. We describe lessons learnt from detecting and responding to recurrent outbreaks of measles two years post the 2014 Ebola epidemic in Liberia., Methods: We conducted a descriptive study using the findings from Integrated Diseases Surveillance and Response (IDSR) 15 counties, National Public Health Institute of Liberia (NPHIL), National Public Health Reference Laboratory (NPHRL) and District Health Information Software (DIHS2) data conducted from October to December, 2017. We perused the outbreaks line lists and other key documents submitted by the counties to the national level from January 2016 to December 2017., Results: From January 2016 to December 2017, 2,954 suspected cases of measles were reported through IDSR. Four hundred sixty-seven (467) were laboratory confirmed (IgM-positive), 776 epidemiologically linked, 574 clinically confirmed, and 1,137 discarded (IgM-negative). Nine deaths out of 1817 cases were reported, a case fatality rate of 0.5%; 49% were children below the age of 5 years. Twenty-two percent (405/1817) of the confirmed cases were vaccinated while the vaccination status of 55% (994/1817) was unknown., Conclusion: Revitalization of IDSR contributed to increased detection and reporting of suspected cases of measles thus facilitating early identification and response to outbreaks. Priority needs to be given to increasing the uptake of routine immunization services, introducing a second dose of measles vaccine in the routine immunization program and conducting a high-quality supplementary measles immunization campaign for age group 1 to 10 years to provide protection for a huge cohort of susceptible., Competing Interests: The authors declare no competing interest.

Introduction: Lessons learned from the Ebola virus disease (EVD) outbreak enabled Liberia to develop a health plan for strengthening public health capacity against potential public health threats. risk communication is one of the core pillars that provide life-saving information and knowledge for the public to take preventive and proactive actions against public health threats. These were applied in response to the post-ebola meningococcal septicemia and meningitis outbreaks in Sinoe and Grand Kru counties. This paper documents risk communication experiences in these post-ebola outbreaks in Liberia., Methods: Risk Communication and health promotion strategies were deployed in developing response plans and promptly disseminating key messages to affected communities to mitigate the risks. Other strategies included engagement of community leaders, partnership with the media and dissemination of messages through the community radios, active monitoring community risk perceptions and compliance, rumor management, mobile stage and interpersonal communication (IPC) during the Meningococcal disease outbreaks in Sinoe and Grand Kru counties., Results: In Sinoe, about 36,891 households or families in 10 health districts were reached through IPC and dialogue. Circulating rumors such as "Ebola" was the cause of deaths was timely and promptly mitigated. There was increased trust and adherence to health advice including prompt reporting of sick people to the nearest health facility in the two counties., Conclusion: Risk communication and health promotion encouraged community support and involvement in any response to public threats and events. No doubt, risk communication and health promotion play an important role in preparedness and response to public health emergencies., Competing Interests: The authors declare no competing interest.

Introduction: The Ebola virus disease (EVD) outbreak in Liberia from 2014-2015 setback the already fragile health system which was recovering from the effects of civil unrest. This led to significant decline in immunization coverage and key polio free certification indicators. The Liberia investment plan was developed to restore immunization service delivery and overall health system., Methods: We conducted a desk review to summarize performance of immunization coverage, polio eradication, measles control, new vaccines and technologies. Data sources include program reports, scientific and grey literature, District Health Information System (DHIS2), Integrated Diseases Surveillance and Response (IDSR) database, auto visual AFP detection and reporting (AVADAR) and ONA Servers. Data analysis was done using Microsoft excel spreadsheets, ONA software and Arc GIS., Results: There was a 36% increase in national coverage for Penta 3 in 2017 compared to 2014 from WUENIC data. Penta 3 dropout rate reduced by 2.5 fold from 15.3% in 2016 to 6.4% in 2017; while MCV1 coverage improved by 23% from 64% in 2015 to 87% in 2017. There was a rebound of non-polio AFP rate (NPAFP) rate from 1.2 in 2015 to 4.3 in 2017. Furthermore, there was a 2-fold increase in the number of AFP cases receiving 3 or more doses of OPV from 36% in 2015 to 61% in 2017., Conclusion: Liberia demonstrated strong rebound of immunization services following the largest and most devastating EVD outbreak in West Africa in 2014 - 2015. Immunization coverage improved and dropout rates reduced. However, there are still opportunities for improvement in the immunization program both at national and sub-national levels., Competing Interests: The authors declare no competing interest.

Introduction: Although Liberia adapted the integrated diseases surveillance and response (IDSR) in 2004 as a platform for implementation of International Health Regulation (IHR (2005)), IDSR was not actively implemented until 2015. Some innovations and best practices were observed during the implementation of IDSR in Liberia after Ebola virus disease outbreak. This paper describes the different approaches used for implementation of IDSR in Liberia from 2015 to 2017., Methods: We conducted a cross-sectional study using the findings from IDSR supervisions conducted from September to November 2017 and perused the outbreaks linelists submitted by the counties to the national level from January to December 2017 and key documents available at the national level., Results: In 2017, the country piloted the use of mobile phones application to store and send data from the health facilities to the national level. In addition, an electronic platform for acute flaccid paralysis (AFP) surveillance called Auto-Visual AFP Detection and Reporting (AVADAR) was piloted in Montserrado County during the first semester of 2017. The timeliness and completeness of reports submitted from the counties to national level were above the target of 80% stable despite the challenges like insufficient resources, including skilled staff., Conclusion: IDSR is being actively implemented in Liberia since 2015. Although the country is facing the same challenges as other countries during the early stages of implementation of IDSR, the several innovations were implemented in a short time. The surveillance system reveled to be resilient, despite the challenges., Competing Interests: The authors declare no competing interest.

Introduction: Liberia remains at high risk of poliovirus outbreaks due to importation. The country maintained certification level acute flaccid paralysis (AFP) surveillance indicators each year until 2014 due to Ebola outbreak. During this time, there was a significant drop in non-polio AFP rate to (1.2/100,000 population under 15 years) in 2015 from 2.9/100, 000 population in 2013, due to a variety of reasons including suspension on shipment of acute flaccid paralysis stool specimen to the polio regional lab in Abidjan, refocusing of surveillance officers attention solely on Ebola virus disease (EVD) surveillance, inactivation of national polio expert committee (NPEC) and National Certification Committee (NCC). The Ministry of Health (MOH) supported by partners worked to restore AFP surveillance post EVD outbreak and ensure that Liberia maintains its polio free certification., Methods: We conducted a desk review to summarize key activities conducted to restore acute flaccid paralysis (AFP) surveillance based on World Health Organization (WHO) AFP surveillance guidelines for Africa region. We also reviewed AFP surveillance indicators and introduction of new technologies. Data sources were from program reports, scientific and gray literature, AFP database, auto visual AFP detection and reporting (AVADAR) and ONA Servers. Data analysis was done using Microsoft excel and access spread sheets, ONA software and Geographic Information System (Arc GIS)., Results: AFP surveillance indicators improved with a rebound of non-polio AFP rate (NPAFP) rate from 1.2/100, 000 population under 15 years in 2015 to 4.3 in 2017. The stool adequacy rate at the national level also improved from 79% in 2016 to 82% in 2017, meeting the global target. The percentage of counties meeting the two critical AFP surveillance indicators NPAFP rate and stool adequacy improved from 47% in 2016 to 67% in 2017.The Last polio case reported in Liberia was in late 2010., Conclusion: There was significant improvement in the key AFP surveillance indicators such as NPAFP rate and stool adequacy with a 3.5 fold increase in NPAFP from 2014 to 2017. By 2017, the stool adequacy rate was up to target levels compared to 2016, which was below target level of 80%. The number of counties meeting target for the two critical AFP surveillance indicators also increased by 20% points between 2016 and 2017. Similarly there was approximately two-fold increase in the oral polio vaccines (OPV) coverage for the reported AFP cases between 2015 and 2017. Strategies employed to address gaps in AFP surveillance included enhanced active case search for AFP, re-instatement of laboratory testing, supportive supervision in addition to facilitating enhanced community engagement in surveillance activities. New technologies such as AVADAR Pilot, electronic integrated supportive supervision (ISS) and electronic surveillance (eSurv) tools were introduced to improve real time AFP case reporting. However, there remain residual gaps in AFP surveillance in the country especially at the sub-national level. Similarly, the newly introduced technologies will require continued funding and capacity building for MOH staff to ensure sustainability of the initiatives., Competing Interests: The authors declare no competing interest.

Background: The Ministry of Health and Sanitation (MOHS) in Sierra Leone partially rolled out the implementation of Integrated Disease Surveillance and Response (IDSR) in 2003. After the Ebola virus disease outbreak in 2014-2015, there was need to strengthen IDSR to ensure prompt detection and response to epidemic-prone diseases. We describe the processes, successes and challenges of revitalizing public health surveillance in a country recovering from a protracted Ebola virus disease outbreak., Methods: The revitalization process began with adaptation of the revised IDSR guidelines and development of customized guidelines to suit the health care systems in Sierra Leone. Public health experts defined data flow, system operations, case definitions, frequency and channels of reporting and dissemination. Next, phased training of IDSR focal persons in each health facility and the distribution of data collection and reporting tools was done. Monitoring activities included periodic supportive supervision and data quality assessments. Rapid response teams were formed to investigate and respond to disease outbreak alerts in all districts., Results: Submission of reports through the IDSR system began in mid-2015 and by the 35th epidemiologic week, all district health teams were submitting reports. The key performance indicators measuring the functionality of the IDSR system in 2016 and 2017 were achieved (WHO Africa Region target ≥80%); the annual average proportion of timely weekly health facility reports submitted to the next level was 93% in 2016 and 97% in 2017; the proportion of suspected outbreaks and public health events detected through the IDSR system was 96% (n = 87) in 2016 and 100% (n = 85) in 2017., Conclusion: With proper planning, phased implementation and adequate investment of resources, it is possible to establish a functional IDSR system in a country recovering from a public health crisis. A functional IDSR system requires well trained workforce, provision of the necessary tools and guidelines, information, communication and technology infrastructure to support data transmission, provision of timely feedback as well as logistical support.

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., Competing Interests: The authors have declared that no competing interests exist.

Background: Influenza is an acute viral disease of the respiratory tract which is characterized by fever, headache, myalgia, prostration, coryza, sore throat and cough. Globally, an estimated 3 to 5 million cases of severe influenza illness and 291 243-645 832 seasonal influenza-associated respiratory deaths occur annually. Although recent efforts from some African countries to describe burden of influenza disease and seasonality, these data are missing for the vast majority, including Ethiopia. Ethiopia established influenza sentinel surveillance in 2008 aiming to determine influenza strains circulating in the country and know characteristics, trend and burden of influenza viruses., Methods: We used influenza data from sentinel surveillance sites and respiratory disease outbreak investigations from 2009 to 2015 for this analysis. We obtained the data by monitoring patients with influenza-like illness (ILI) at three health-centers, severe acute respiratory infection (SARI) at five hospitals and investigating patients during different respiratory infection outbreaks. Throat-swab specimens in viral transport media were transported to the national reference laboratory within 72 h of collection using a cold-chain system. We extracted viral RNA from throat-swabs and subjected to real-time PCR amplification. We further subtyped and characterized Influenza A-positive specimens using CDC real-time reverse transcription PCR protocol., Results: A total of 4962 throat-swab samples were collected and 4799 (96.7%) of them were tested. Among them 988 (20.6%) were influenza-positive and of which 349 (35.3%) were seasonal influenza A(H3N2), 321 (32.5%) influenza A(H1N1)pdm2009 and 318 (32.0%) influenza B. Positivity rate was 29.5% in persons 5-14 years followed by 26.4% in 15-44 years, 21.2% in > 44 years and 6.4% in under five children. The highest positivity rate observed in November (37.5%) followed by March (27.6%), December (26.4%), October (24.4%) and January (24.3%) while the lowest positivity rate was in August (7.7%)., Conclusion: In Ethiopia, seasonal Influenza A(H3N2), Influenza A(H1N1)pdm2009 and Influenza B viruses were circulating during 2009-2015. Positivity rate and number of cases peaked in November and December. Influenza is one of public health problems in Ethiopia and the need to introduce influenza vaccine and antivirus is important to prevent and treat the disease in future.

Background: Data on causes of death due to respiratory illness in Africa are limited., Methods: From January to April 2013, 28 African countries were invited to participate in a review of severe acute respiratory illness (SARI)-associated deaths identified from influenza surveillance during 2009-2012., Results: Twenty-three countries (82%) responded, 11 (48%) collect mortality data, and 8 provided data. Data were collected from 37 714 SARI cases, and 3091 (8.2%; range by country, 5.1%-25.9%) tested positive for influenza virus. There were 1073 deaths (2.8%; range by country, 0.1%-5.3%) reported, among which influenza virus was detected in 57 (5.3%). Case-fatality proportion (CFP) was higher among countries with systematic death reporting than among those with sporadic reporting. The influenza-associated CFP was 1.8% (57 of 3091), compared with 2.9% (1016 of 34 623) for influenza virus-negative cases (P < .001). Among 834 deaths (77.7%) tested for other respiratory pathogens, rhinovirus (107 [12.8%]), adenovirus (64 [6.0%]), respiratory syncytial virus (60 [5.6%]), and Streptococcus pneumoniae (57 [5.3%]) were most commonly identified. Among 1073 deaths, 402 (37.5%) involved people aged 0-4 years, 462 (43.1%) involved people aged 5-49 years, and 209 (19.5%) involved people aged ≥50 years., Conclusions: Few African countries systematically collect data on outcomes of people hospitalized with respiratory illness. Stronger surveillance for deaths due to respiratory illness may identify risk groups for targeted vaccine use and other prevention strategies., (Published by Oxford University Press on behalf of the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Background: Leptospirosis is a widespread but underreported cause of morbidity and mortality. It has rarely been reported in either humans or animals in Madagascar., Methods: We conducted a cross-sectional survey of the inhabitants in Moramanga, Madagascar, in June 2011, to estimate the prevalence of human infection using the microscopic agglutination test (MAT). This activity was carried out as part of a workshop implemented by the Pasteur Institute of Madagascar, focusing on surveillance with a one week field study and targeting the health staff of the district level., Results: In total, we sampled 678 inhabitants from 263 households. The sex ratio (M/F) was 0.65 and the mean age 26.7 years. We obtained a value of 2.9% for the first recorded seroprevalence of this disease in the human community of Moramanga. Questionnaire responses revealed frequent contacts between humans and rodents in Moramanga. However, activities involving cattle were identified as a risk factor significantly associated with seropositivity (OR=3)., Conclusion: Leptospirosis remains a neglected disease in Madagascar. This study highlights the need to quantify the public health impact of this neglected disease in a more large scale, in all the country and to establish point-of-care laboratories in remote areas.

Background: Epidemics pose major threats in resource-poor countries, and surveillance tools for their early detection and response are often inadequate. In 2007, a sentinel surveillance system was established in Madagascar, with the aim of rapidly identifying potential epidemics of febrile or diarrhoeal syndromes and issuing alerts. We present the health and process indicators for the five years during which this system was constructed, showing the spatiotemporal trends, early-warning sign detection capability and process evaluation through timely analyses of high-quality data., Methods: The Malagasy sentinel surveillance network is currently based on data for fever and diarrhoeal syndromes collected from 34 primary health centres and reported daily via the transmission of short messages from mobile telephones. Data are analysed daily at the Institut Pasteur de Madagascar to make it possible to issue alerts more rapidly, and integrated process indicators (timeliness, data quality) are used to monitor the system., Results: From 2007 to 2011, 917,798 visits were reported. Febrile syndromes accounted for about 11% of visits annually, but the trends observed differed between years and sentinel sites. From 2007 to 2011, 21 epidemic alerts were confirmed. However, delays in data transmission were observed (88% transmitted within 24 hours in 2008; 67% in 2011) and the percentage of forms transmitted each week for validity control decreased from 99.9% in 2007 to 63.5% in 2011., Conclusion: A sentinel surveillance scheme should take into account both epidemiological and process indicators. It must also be governed by the main purpose of the surveillance and by local factors, such as the motivation of healthcare workers and telecommunication infrastructure. Permanent evaluation indicators are required for regular improvement of the system.

Background: Tuberculosis continues to cause unacceptably high levels of disease and death worldwide. Active preventive strategies are required to improve tuberculosis control and to increase the number of cases treated in developing countries. The aim of this study was to evaluate the utility of the tuberculin skin test (TST) in first-year schoolchildren as a means of increasing the number of tuberculosis cases detected through the screening of close contacts., Methods: All members of the households of 90 schoolchildren assigned to three groups on the basis of TST category (≤ 5 mm, [5-15)mm, ≥ 15 mm) were screened for sputum smear-positive pulmonary tuberculosis. The percentage detection of tuberculosis in close contacts was compared between TST categories., Results: We identified 433 close contacts of the 90 schoolchildren, who were then evaluated for tuberculosis. We identified 11 cases of pulmonary tuberculosis among the close contacts (7 already on treatment and 4 previously undiagnosed): 0 in TST category ≤ 5 mm, 3 in TST category [5-15) mm and 8 in TST category ≥ 15 mm). This approach increased the detection of tuberculosis cases by a factor of 1.6 in first-year schoolchildren of the TST ≥ 5 mm group., Conclusion: TST in first-year schoolchildren is a potentially effective method for improving the detection of tuberculosis in close contacts.

Background: Diarrheal diseases are a major public health problem in developing countries, and are one of the main causes of hospital admissions in Madagascar. The Pasteur Institute of Madagascar undertook a study to determine the prevalence and the pathogenicity of bacterial, viral and protozoal enteropathogens in diarrheal and non-diarrheal stools of children aged less than 5 years in Madagascar. We present here the results of the analysis of antimicrobial susceptibility of the bacteria isolated during this study., Methods: The study was conducted in the community setting in 14 districts of Madagascar from October 2008 to May 2009. Conventional methods and PCR were used to identify the bacteria; antimicrobial susceptibility was determined using an agar diffusion method for enterobacteriaceae and MICs were measured by an agar dilution method for Campylobacter sp. In addition to the strains isolated during this study, Salmonella sp and Shigella sp isolated at the Pasteur Institute of Madagascar from 2005 to 2009 were included in the analysis to increase the power of the study., Results: Twenty-nine strains of Salmonella sp, 35 strains of Shigella sp, 195 strains of diarrheagenic E. coli, 203 strains of C. jejuni and 71 strains of C. coli isolated in the community setting were tested for antibiotic resistance. Fifty-five strains of Salmonella sp and 129 strains of Shigella sp isolated from patients referred to the Pasteur Institute of Madagascar were also included in the study. Many E. coli and Shigella isolates (around 80%) but fewer Salmonella isolates were resistant to ampicillin and trimethoprim/sulfamethoxazole. A small proportion of strains of each species were resistant to ciprofloxacin and only 3% of E. coli strains presented a resistance to third generation cephalosporins due to the production of extended-spectrum beta-lactamases. The resistance of Campylobacter sp to ampicillin was the most prevalent, whereas less than 5% of isolates were resistant to each of the other antibiotics., Conclusion: The highest prevalence of antimicrobial resistance was to ampicillin and trimethoprim/sulfamethoxazole. Antibiotic treatment is not recommended for children with diarrhea in Madagascar and the emphasis should be placed on oral rehydration.

Background: Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. In these low-income countries, most patients with acute respiratory infection (ARI), whether it is mild or severe, are still treated empirically. The aim of the study was to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old., Materials and Methods: We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. We collected demographic, socio-economic, clinical and epidemiological data, and samples for laboratory analysis. Deaths, rapid progression to respiratory distress during hospitalisation, and hospitalisation for more than 10 days were considered as severe outcomes. We used multivariate analysis to study the effects of co-infections., Results: From November 2010 to July 2012, a total of 290 patients were enrolled. Co-infection was found in 192 patients (70%). Co-infections were more frequent in children under 36 months, with a significant difference for the 19-24 month-old group (OR: 8.0). Sixty-nine percent (230/290) of the patients recovered fully and without any severe outcome during hospitalisation; the outcome was scored as severe for 60 children and nine patients (3%) died. Risk factors significantly associated with worsening evolution during hospitalisation (severe outcome) were admission at age under 6 months (OR = 5.3), comorbidity (OR = 4.6) and low household income (OR = 4.1)., Conclusion: Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. These results highlight the need for implementation of targeted public health policy to reduce the contribution of respiratory diseases to childhood morbidity and mortality in low income countries.

Background: Madagascar was one of the first African countries to be affected by the 2009 pandemic of influenza A virus subtype H1N1 [A(H1N1)pdm2009] infection. The outbreak started in the capital city, Antananarivo, and then spread throughout the country from October 2009 through February 2010., Methods: Specimens from patients presenting with influenza-like illness were collected and shipped to the National Influenza Center in Madagascar for analyses, together with forms containing patient demographic and clinical information., Results: Of the 2303 specimens tested, 1016 (44.1%) and 131 (5.7%) yielded A(H1N1)pdm09 and seasonal influenza virus, respectively. Most specimens (42.0%) received were collected from patients <10 years old. Patients <20 years old were more likely than patients >50 years old to be infected with A(H1N1)pdm09 (odds ratio, 2.1; 95% confidence interval, 1.7-2.6; P < .01). Although phylogenetic analyses of A(H1N1)pdm09 suggested multiple introductions of the virus into Madagascar, no antigenic differences between A(H1N1)pdm09 viruses recovered in Madagascar and those that circulated worldwide were observed., Conclusions: The high proportion of respiratory specimens positive for A(H1N1)pdm09 is consistent with a widespread transmission of the pandemic in Madagascar. The age distribution of cases of A(H1N1)pdm09 infection suggests that children and young adults could be targeted for interventions that aim to reduce transmission during an influenza pandemic.

Problem: The revision of the International Health Regulations (IHR) and the threat of influenza pandemics and other disease outbreaks with a major impact on developing countries have prompted bolstered surveillance capacity, particularly in low-resource settings., Approach: Surveillance tools with well-timed, validated data are necessary to strengthen disease surveillance. In 2007 Madagascar implemented a sentinel surveillance system for influenza-like illness (ILI) based on data collected from sentinel general practitioners., Setting: Before 2007, Madagascar's disease surveillance was based on the passive collection and reporting of data aggregated weekly or monthly. The system did not allow for the early identification of outbreaks or unexpected increases in disease incidence., Relevant Changes: An innovative case reporting system based on the use of cell phones was launched in March 2007. Encrypted short message service, which costs less than 2 United States dollars per month per health centre, is now being used by sentinel general practitioners for the daily reporting of cases of fever and ILI seen in their practices. To validate the daily data, practitioners also report epidemiological and clinical data (e.g. new febrile patient's sex, age, visit date, symptoms) weekly to the epidemiologists on the research team using special patient forms., Lessons Learnt: Madagascar's sentinel ILI surveillance system represents the country's first nationwide "real-time" surveillance system. It has proved the feasibility of improving disease surveillance capacity through innovative systems despite resource constraints. This type of syndromic surveillance can detect unexpected increases in the incidence of ILI and other syndromic illnesses.

Background: The influenza A(H1N1)pdm09 virus has been a challenge for public health surveillance systems in all countries. In Antananarivo, the first imported case was reported on August 12, 2009. This work describes the spread of A(H1N1)pdm09 in Madagascar., Methods: The diffusion of influenza A(H1N1)pdm09 in Madagascar was explored using notification data from a sentinel network. Clinical data were charted to identify peaks at each sentinel site and virological data was used to confirm viral circulation., Results: From August 1, 2009 to February 28, 2010, 7,427 patients with influenza-like illness were reported. Most patients were aged 7 to 14 years. Laboratory tests confirmed infection with A(H1N1)pdm09 in 237 (33.2%) of 750 specimens. The incidence of patients differed between regions. By determining the epidemic peaks we traced the diffusion of the epidemic through locations and time in Madagascar. The first peak was detected during the epidemiological week 47-2009 in Antananarivo and the last one occurred in week 07-2010 in Tsiroanomandidy., Conclusion: Sentinel surveillance data can be used for describing epidemic trends, facilitating the development of interventions at the local level to mitigate disease spread and impact.

Background: Acute diarrhea is a major cause of childhood morbidity and mortality worldwide. Its microbiological causes and clinico-epidemiological aspects were examined during the rainy seasons from 2008 to 2009 in 14 districts in Madagascar., Methods: Stool specimens of 2196 children with acute diarrhea and 496 healthy children were collected in a community setting. Intestinal parasites were diagnosed by microscopy and bacteria by culturing methods. Rota-, astro and adenoviruses were identified using commercially available ELISA kits and rotaviruses were confirmed using reverse transcriptase polymerase chain reaction (RT-PCR)., Results: Intestinal microorganisms were isolated from 54.6% of diarrheal patients and 45.9% of healthy subjects (p = <0.01). The most common pathogens in diarrheic patients were intestinal parasites (36.5%). Campylobacter spp. and Rotavirus were detected in 9.7% and 6.7% of diarrheic patients. The detection rates of Entamoeba histolytica, Trichomonas intestinalis and Giardia lamblia were much greater in diarrheal patients than in non diarrheal subjects (odds ratios of 5.1, 3.2, 1.7 respectively). The abundance of other enteropathogens among the non diarrheal group may indicate prolonged excretion or limited pathogenicity., Conclusion: In developing countries, where the lack of laboratory capacities is great, cross sectional studies of enteropathogens and their spatial distribution, including diarrheal and non diarrheal subjects, are interesting tools in order to advise regional policies on treatment and diarrheic patient management.

Introduction: In October 2009, the first outbreak of pandemic influenza A(H1N1) 2009 virus  in Madagascar occurred at a school in Antananarivo. Among the first 12 cases, five were reported in boarding pupils at the school. The school closed 10 days into the outbreak. Mass oseltamivir prophylactic treatment was used to contain the outbreak. This study aimed to determine the transmission of infection among boarding school pupils and to evaluate the adverse effects of oseltamivir chemoprophylactic treatment and their impact on compliance., Methodology: After conducting an initial investigation of the outbreak we administered a questionnaire to 132 boarders who were present after the school re-opened. Questions addressed symptoms of influenza-like illness, compliance with chemoprophylaxis, and adverse effects., Results: Of 59 boarders, 20 (45.0%) had confirmed pandemic influenza A (H1N1) infection. Among the asymptomatic boarders, compliance with oseltamivir chemoprophylaxis was moderate: 56.2% took the full 10-day course, and 66.9% completed at least seven days. In contrast, among symptomatic boarders, only two did not take the full course of oseltamivir. Fifty percent of the boarders receiving oseltamivir experienced symptoms such as fatigue (38.7%), difficulty concentrating (22.6%) and headaches (19.4%). Bad compliance was not associated with adverse effects., Conclusion: Since the symptoms of pandemic influenza A(H1N1) 2009 virus were generally mild, the burden of adverse effects must be considered when deciding on mass oseltamivir chemoprophylaxis among teenagers.