Epidemiology of influenza in Nigeria: A secondary analysis of the sentinel surveillance data in Nigeria from 2010 - 2020

BACKGROUND

Influenza is a leading cause of morbidity and mortality globally. Little is known of the true burden and epidemiology of influenza in Africa. Nigeria has a sentinel surveillance system for influenza virus (IFV). This study seeks to describe the epidemiological characteristics of influenza cases in Nigeria through secondary data analysis of the sentinel surveillance data from 2010 to 2020.

METHODOLOGY

A retrospective secondary data analysis of data collected from patients with influenza-like illness (ILI) and severe acute respiratory infection (SARI) in the four Nigeria Influenza Sentinel Surveillance sites from January 2010 to December 2020. Data was cleaned and analyzed using Microsoft Excel and Epi info 7.2 for frequencies and proportions. The results of the analysis were summarized in tables and charts.

RESULTS

A total of 13,828 suspected cases of influenza were recorded at the sentinel sites during the study period. About 10.3% (1421/13,828) of these tested positive for IFV of which 1243 (87.5%) were ILI patients, 175 (12.3%) SARI patients, and 3 (0.2%) novel H1N1 patients. Males accounted for 54.2% (770/1421) of the confirmed cases. The median age of confirmed cases was 3 years (range: <1month-97 years). Children 0-4 years accounted for 69.3% (985/1421) of all cases. The predominant subtypes were B lineage not determined (32.3%), A/H1N1 pdm09 (28.8%) and A/H3 (23.0%). There were periods of sustained transmission in most years with 2011 having the highest number of cases. Overall, there were more cases around January to March and August to November. Heart disease and chronic shortness of breath were the most common co-morbidities identified among confirmed cases.

CONCLUSION

Influenza remains a significant cause of respiratory illness, especially among children aged less than 4 years. Influenza cases occur all year round with irregular seasonality in Nigeria. Children less than 4 years and those with co-morbidities should be prioritized for vaccination. Vaccine composition in the country should take cognizance of the prevailing strains which are type B (lineage not determined), A/H1N1 pdm09 and A/H3.

Cholera past and future in Nigeria: Are the Global Task Force on Cholera Control's 2030 targets achievable?

BACKGROUND

Understanding and continually assessing the achievability of global health targets is key to reducing disease burden and mortality. The Global Task Force on Cholera Control (GTFCC) Roadmap aims to reduce cholera deaths by 90% and eliminate the disease in twenty countries by 2030. The Roadmap has three axes focusing on reporting, response and coordination. Here, we assess the achievability of the GTFCC targets in Nigeria and identify where the three axes could be strengthened to reach and exceed these goals.

METHODOLOGY/PRINCIPAL FINDINGS

Using cholera surveillance data from Nigeria, cholera incidence was calculated and used to model time-varying reproduction number (R). A best fit random forest model was identified using R as the outcome variable and several environmental and social covariates were considered in the model, using random forest variable importance and correlation clustering. Future scenarios were created (based on varying degrees of socioeconomic development and emission reductions) and used to project future cholera transmission, nationally and sub-nationally to 2070. The projections suggest that significant reductions in cholera cases could be achieved by 2030, particularly in the more developed southern states, but increases in cases remain a possibility. Meeting the 2030 target, nationally, currently looks unlikely and we propose a new 2050 target focusing on reducing regional inequities, while still advocating for cholera elimination being achieved as soon as possible.

CONCLUSION/SIGNIFICANCE

The 2030 targets could potentially be reached by 2030 in some parts of Nigeria, but more effort is needed to reach these targets at a national level, particularly through access and incentives to cholera testing, sanitation expansion, poverty alleviation and urban planning. The results highlight the importance of and how modelling studies can be used to inform cholera policy and the potential for this to be applied in other contexts.

A prospective, multi-site, cohort study to estimate incidence of infection and disease due to Lassa fever virus in West African countries (the Enable Lassa research programme)-Study protocol

BACKGROUND

Lassa fever (LF), a haemorrhagic illness caused by the Lassa fever virus (LASV), is endemic in West Africa and causes 5000 fatalities every year. The true prevalence and incidence rates of LF are unknown as infections are often asymptomatic, clinical presentations are varied, and surveillance systems are not robust. The aim of the Enable Lassa research programme is to estimate the incidences of LASV infection and LF disease in five West African countries. The core protocol described here harmonises key study components, such as eligibility criteria, case definitions, outcome measures, and laboratory tests, which will maximise the comparability of data for between-country analyses.

METHOD

We are conducting a prospective cohort study in Benin, Guinea, Liberia, Nigeria (three sites), and Sierra Leone from 2020 to 2023, with 24 months of follow-up. Each site will assess the incidence of LASV infection, LF disease, or both. When both incidences are assessed the LASV cohort (nmin = 1000 per site) will be drawn from the LF cohort (nmin = 5000 per site). During recruitment participants will complete questionnaires on household composition, socioeconomic status, demographic characteristics, and LF history, and blood samples will be collected to determine IgG LASV serostatus. LF disease cohort participants will be contacted biweekly to identify acute febrile cases, from whom blood samples will be drawn to test for active LASV infection using RT-PCR. Symptom and treatment data will be abstracted from medical records of LF cases. LF survivors will be followed up after four months to assess sequelae, specifically sensorineural hearing loss. LASV infection cohort participants will be asked for a blood sample every six months to assess LASV serostatus (IgG and IgM).

DISCUSSION

Data on LASV infection and LF disease incidence in West Africa from this research programme will determine the feasibility of future Phase IIb or III clinical trials for LF vaccine candidates.

An assessment of infection prevention and control preparedness of healthcare facilities in Nigeria in the early phase of the COVID-19 pandemic (February–May 2020)

Background

Infection prevention and control (IPC) activities play a large role in preventing the transmission of SARS-CoV-2 in healthcare settings. This study describes the state of IPC preparedness within health facilities in Nigeria during the early phase of coronavirus disease (COVID-19) pandemic.

Methods

We carried out a cross sectional study of health facilities across Nigeria using a COVID-19 IPC checklist adapted from the U.S Centers for Disease Control and Prevention. The IPC aspects assessed were the existence of IPC committee and teams with terms of reference and workplans, IPC training, availability of personal protective equipment and having systems in place for screening, isolation and notification of COVID-19 patients. Existence of the assessed aspects was regarded as preparedness in that aspect.

Results

In total, 461 health facilities comprising, 350 (75.9%) private and 111 (24.1%) public health facilities participated. Only 19 (4.1%) health facilities were COVID-19 treatment centres with 68% of these being public health facilities. Public health facilities were better prepared in the areas of IPC programme with 69.7% of them having an IPC focal point versus 32.3% of private facilities. More public facilities (59.6%) had an IPC workplan versus 26.8% of private facilities. Neither the public nor the private facilities were adequately prepared for triaging, screening, and notifying suspected cases, as well as having trained staff and equipment to implement triaging.

Conclusions

The results highlight the need for government, organisations and policymakers to establish conducive IPC structures to reduce the risk of COVID-19 transmission in healthcare settings.

Seroprevalence of SARS-CoV-2 in four states of Nigeria in October 2020: A population-based household survey

The observed epidemiology of SARS-CoV-2 in sub-Saharan Africa has varied greatly from that in Europe and the United States, with much lower reported incidence. Population-based studies are needed to estimate true cumulative incidence of SARS-CoV-2 to inform public health interventions. This study estimated SARS-CoV-2 seroprevalence in four selected states in Nigeria in October 2020. We implemented a two-stage cluster sample household survey in four Nigerian states (Enugu, Gombe, Lagos, and Nasarawa) to estimate age-stratified prevalence of SARS-CoV-2 antibodies. All individuals in sampled households were eligible for interview, blood draw, and nasal/oropharyngeal swab collection. We additionally tested participants for current/recent malaria infection. Seroprevalence estimates were calculated accounting for the complex survey design. Across all four states, 10,629 (96·5%) of 11,015 interviewed individuals provided blood samples. The seroprevalence of SARS-CoV-2 antibodies was 25·2% (95% CI 21·8-28·6) in Enugu State, 9·3% (95% CI 7·0-11·5) in Gombe State, 23·3% (95% CI 20·5-26·4) in Lagos State, and 18·0% (95% CI 14·4-21·6) in Nasarawa State. Prevalence of current/recent malaria infection ranged from 2·8% in Lagos to 45·8% in Gombe and was not significantly related to SARS-CoV-2 seroprevalence. The prevalence of active SARS-CoV-2 infection in the four states during the survey period was 0·2% (95% CI 0·1-0·4). Approximately eight months after the first reported COVID-19 case in Nigeria, seroprevalence indicated infection levels 194 times higher than the 24,198 officially reported COVID-19 cases across the four states; however, most of the population remained susceptible to COVID-19 in October 2020.

Analysis of sociodemographic and clinical factors associated with Lassa fever disease and mortality in Nigeria

Over past decades, there has been increasing geographical spread of Lassa fever (LF) cases across Nigeria and other countries in West Africa. This increase has been associated with significant morbidity and mortality despite increasing focus on the disease by both local and international scientists. Many of these studies on LF have been limited to few specialised centres in the country. This study was done to identify sociodemographic and clinical predictors of LF disease and related deaths across Nigeria. We analysed retrospective surveillance data on suspected LF cases collected during January-June 2018 and 2019. Multivariable logistic regression analyses were used to identify the factors independently associated with laboratory-confirmed LF diagnosis, and with LF-related deaths. There were confirmed 815 of 1991 suspected LF cases with complete records during this period. Of these, 724/815 confirmed cases had known clinical outcomes, of whom 100 died. LF confirmation was associated with presentation of gastrointestinal tract (aOR 3.47, 95% CI: 2.79-4.32), ear, nose and throat (aOR 2.73, 95% CI: 1.80-4.15), general systemic (aOR 2.12, 95% CI: 1.65-2.70) and chest/respiratory (aOR 1.71, 95% CI: 1.28-2.29) symptoms. Other factors were being male (aOR 1.32, 95% CI: 1.06-1.63), doing business/trading (aOR 2.16, 95% CI: 1.47-3.16) and farming (aOR 1.73, 95% CI: 1.12-2.68). Factors associated with LF mortality were a one-year increase in age (aOR 1.03, 95% CI: 1.01-1.04), bleeding (aOR 2.07, 95% CI: 1.07-4.00), and central nervous manifestations (aOR 5.02, 95% CI: 3.12-10.16). Diverse factors were associated with both LF disease and related death. A closer look at patterns of clinical variables would be helpful to support early detection and management of cases. The findings would also be useful for planning preparedness and response interventions against LF in the country and region.

COVID-19 mortality rate and its associated factors during the first and second waves in Nigeria

COVID-19 mortality rate has not been formally assessed in Nigeria. Thus, we aimed to address this gap and identify associated mortality risk factors during the first and second waves in Nigeria. This was a retrospective analysis of national surveillance data from all 37 States in Nigeria between February 27, 2020, and April 3, 2021. The outcome variable was mortality amongst persons who tested positive for SARS-CoV-2 by Reverse-Transcriptase Polymerase Chain Reaction. Incidence rates of COVID-19 mortality was calculated by dividing the number of deaths by total person-time (in days) contributed by the entire study population and presented per 100,000 person-days with 95% Confidence Intervals (95% CI). Adjusted negative binomial regression was used to identify factors associated with COVID-19 mortality. Findings are presented as adjusted Incidence Rate Ratios (aIRR) with 95% CI. The first wave included 65,790 COVID-19 patients, of whom 994 (1∙51%) died; the second wave included 91,089 patients, of whom 513 (0∙56%) died. The incidence rate of COVID-19 mortality was higher in the first wave [54∙25 (95% CI: 50∙98-57∙73)] than in the second wave [19∙19 (17∙60-20∙93)]. Factors independently associated with increased risk of COVID-19 mortality in both waves were: age ≥45 years, male gender [first wave aIRR 1∙65 (1∙35-2∙02) and second wave 1∙52 (1∙11-2∙06)], being symptomatic [aIRR 3∙17 (2∙59-3∙89) and 3∙04 (2∙20-4∙21)], and being hospitalised [aIRR 4∙19 (3∙26-5∙39) and 7∙84 (4∙90-12∙54)]. Relative to South-West, residency in the South-South and North-West was associated with an increased risk of COVID-19 mortality in both waves. In conclusion, the rate of COVID-19 mortality in Nigeria was higher in the first wave than in the second wave, suggesting an improvement in public health response and clinical care in the second wave. However, this needs to be interpreted with caution given the inherent limitations of the country's surveillance system during the study.

The impact of social and environmental extremes on cholera time varying reproduction number in Nigeria

Nigeria currently reports the second highest number of cholera cases in Africa, with numerous socioeconomic and environmental risk factors. Less investigated are the role of extreme events, despite recent work showing their potential importance. To address this gap, we used a machine learning approach to understand the risks and thresholds for cholera outbreaks and extreme events, taking into consideration pre-existing vulnerabilities. We estimated time varying reproductive number (R) from cholera incidence in Nigeria and used a machine learning approach to evaluate its association with extreme events (conflict, flood, drought) and pre-existing vulnerabilities (poverty, sanitation, healthcare). We then created a traffic-light system for cholera outbreak risk, using three hypothetical traffic-light scenarios (Red, Amber and Green) and used this to predict R. The system highlighted potential extreme events and socioeconomic thresholds for outbreaks to occur. We found that reducing poverty and increasing access to sanitation lessened vulnerability to increased cholera risk caused by extreme events (monthly conflicts and the Palmers Drought Severity Index). The main limitation is the underreporting of cholera globally and the potential number of cholera cases missed in the data used here. Increasing access to sanitation and decreasing poverty reduced the impact of extreme events in terms of cholera outbreak risk. The results here therefore add further evidence of the need for sustainable development for disaster prevention and mitigation and to improve health and quality of life.

The One Health approach to incident management of the 2019 Lassa fever outbreak response in Nigeria

Globally, effective emergency response to disease outbreaks is usually affected by weak coordination. However, coordination using an incident management system (IMS) in line with a One Health approach involving human, environment, and animal health with collaborations between government and non-governmental agencies result in improved response outcome for zoonotic diseases such as Lassa fever (LF).

We provide an overview of the 2019 LF outbreak response in Nigeria using the IMS and One Health approach. The response was coordinated via ten Emergency Operation Centre (EOC) response pillars. Cardinal response activities included activation of EOC, development of an incident action plan, deployment of One Health rapid response teams to support affected states, mid-outbreak review and after-action review meetings.

Between 1st January and 29th December 2019, of the 5057 people tested for LF, 833 were confirmed positive from 23 States, across 86 Local Government Areas. Of the 833 confirmed cases, 650 (78%) were from hotspot States of Edo (36%), Ondo (26%) and Ebonyi (16%). Those in the age-group 21–40 years (47%) were mostly affected, with a male to female ratio of 1:1. Twenty healthcare workers were affected. Two LF naïve states Kebbi and Zamfara, reported confirmed cases for the first time during this period.

The outbreak peaked earlier in the year compared to previous years, and the emergency phase of the outbreak was declared over by epidemiological week 17 based on low national threshold composite indicators over a period of six consecutive weeks.

Multisectoral and multidisciplinary strategic One Health EOC coordination at all levels facilitated the swift containment of Nigeria's large LF outbreak in 2019. It is therefore imperative to embrace One Health approach embedded within the EOC to holistically address the increasing LF incidence in Nigeria.

Research as a pillar of Lassa fever emergency response: lessons from Nigeria

Emerging and re-emerging infectious diseases are becoming more frequent and developing countries are especially at increased risk. A recurring infectious disease outbreak in Nigeria has been that of Lassa fever (LF), a disease that is endemic in Nigeria and other West African countries. Nigeria, between 1^st January and 27^th October 2019, reported 743 confirmed cases of LF and 157 deaths in confirmed cases. Lassa fever outbreaks continue to be recurrent after fifty years of its identification. The true burden of the disease in Nigeria is unknown while gaps in knowledge about the infection still persist. Based on the Nigeria national Lassa fever research agenda and the World Health Organisation's roadmap initiative for accelerating research and product development which enables effective and timely emergency response to LF disease epidemics among other infectious diseases; a research pillar was added to the seven existing LF emergency operations centre response pillars in 2019. We describe lessons learnt from the integration of a research pillar into the LF national emergency response.

Field notes from the Nigeria Centre for Disease Control 2019 pilot internship program for resident doctors

The 10-week internship for the pilot cohort of resident doctors from various teaching hospitals in Nigeria was a very rewarding experience. The internship was a beautiful immersion into field epidemiology, rumor surveillance, risk communication, digital tools for surveillance, developing strategic documents, line lists interpretation, weekly presentations and outbreak response coordination alongside working briefly as an incident manager for the Yellow Fever technical working group. Some of the learning points included: meeting coordination, contributions to ongoing research, review of training documents for surveillance officers and the mechanisms of escalating and de-escalating technical working groups in the face of outbreaks and working as an incident manager. There is the need to continue this internship to strengthen the capacity of our emerging health workforce in residency training to address our public health priorities in Nigeria.