The first epidemiological and virological influenza surveillance in the Republic of Guinea revealed the predominance of influenza A/H3N2 and B Victoria viruses.

Little is known about respiratory viruses infection in Guinea. Influenza surveillance has not been implemented in Guinea mainly because of the paucity of laboratory infrastructure and capacity. This paper presents the first influenza surveillance data in Guinea.Swabs were obtained from August 2018 through December 2019 at influenza sentinel sites and transported to the Institut National de Santé Publique for testing. Ribonucleic acid was extracted and tested for the presence of influenza A and B by real-time reverse transcription-polymerase chain reaction (RT-PCR). Positive samples were further characterised to determine the subtypes and lineages of influenza viruses.A total of 862 swabs were collected and tested. Twenty-three per cent of samples tested positive for influenza A and B viruses. Characterisation of positive specimens identified influenza A/H1N1pmd09 (2.5%), influenza A/H3N2 (57.3%), influenza B/Victoria lineage (36.7%) and 7 (3.5%) influenza B with undetermined lineage. Influenza B virus activity clustered in August through November while influenza A/H3N2 displayed two clusters of activities that appeared in May through August and November through December.For the first time in Guinea, the epidemiology, diversity and period of circulation of influenza viruses were studied. The results indicate the predominance and the periods of activities of influenza B Victoria lineage and influenza A/H3N2 which are important information for preventive strategies. It is warranted to extend the influenza surveillance to other parts of Guinea to better understand the epidemiology of the viruses and monitor the emergence of influenza strains with pandemic potential.

Revitalization of integrated disease surveillance and response in Sierra Leone post Ebola virus disease outbreak.

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.

Epidemiology of influenza in Ethiopia: findings from influenza sentinel surveillance and respiratory infection outbreak investigations, 2009-2015.

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.

Antimicrobial resistance of bacterial enteropathogens isolated from stools in Madagascar.

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.

Epidemiological and virological characterization of 2009 pandemic influenza A virus subtype H1N1 in Madagascar.

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.

Transmissibility and severity of COVID-19 in a humanitarian setting: First few X investigation of cases and contacts in Juba, South Sudan, 2020.

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.

Short message service sentinel surveillance of influenza-like illness in Madagascar, 2008-2012.

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.

Early epidemiological investigations: World Health Organization UNITY protocols provide a standardized and timely international investigation framework during the COVID-19 pandemic.

BACKGROUND: The declaration of Coronavirus disease 2019 (COVID-19) as a Public Health Emergency of International Concern (PHEIC) on 30 January 2020 required rapid implementation of early investigations to inform appropriate national and global public health actions. METHODS: The suite of existing pandemic preparedness generic epidemiological early investigation protocols was rapidly adapted for COVID-19, branded the 'UNITY studies' and promoted globally for the implementation of standardized and quality studies. Ten protocols were developed investigating household (HH) transmission, the first few cases (FFX), population seroprevalence (SEROPREV), health facilities transmission (n = 2), vaccine effectiveness (n = 2), pregnancy outcomes and transmission, school transmission, and surface contamination. Implementation was supported by WHO and its partners globally, with emphasis to support building surveillance and research capacities in low- and middle-income countries (LMIC). RESULTS: WHO generic protocols were rapidly developed and published on the WHO website, 5/10 protocols within the first 3 months of the response. As of 30 June 2021, 172 investigations were implemented by 97 countries, of which 62 (64%) were LMIC. The majority of countries implemented population seroprevalence (71 countries) and first few cases/household transmission (37 countries) studies. CONCLUSION: The widespread adoption of UNITY protocols across all WHO regions indicates that they addressed subnational and national needs to support local public health decision-making to prevent and control the pandemic.

Transmission of SARS-CoV-2 in standardised first few X cases and household transmission investigations: A systematic review and meta-analysis.

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.

Institut Pasteur International Network's efforts to guide control measures against the coronavirus disease 2019 (COVID-19) epidemic among healthcare workers in Africa.

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.