The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the WHO to inform the public health response. Real-time analysis of 36 genomes, and subsequent confirmation using all 120 samples sequenced in-country, revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events; allaying concerns of an emergent strain or extensive human-to-human transmission.

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.

Background Lassa fever (LF) is a zoonotic acute viral illness mainly found in West Africa. The disease is endemic in some parts of West Africa including Sierra Leone, Liberia, Guinea and Nigeria; while other neighboring countries at high risk of its outbreak since the animal vectors are distributed throughout the region. Methods This is a retrospective mixed cohort study that analysed the treatment history containing the sociodemographic and clinical characteristics of 52 laboratory-confirmed LF cases that were admitted to the Kenema Government Hospital Lassa Fever Ward (KGHLFW) during 2016 to 2018; i.e. during the post Ebola outbreak in Sierra Leone. The LF patients whose treatment history we analysed came from either within or outside Kenema district were the KGHLFW is located. Results Majority (59.6%, n = 31/52) of the LF cases recorded during the period under review were adults; females (65.4%, n = 34/52). 2016 recorded more (40.4%, n = 21/52) LF cases; 2017 (28.8%, n = 15/52) and 2018(30.8%, n = 16/52). Conclusions We highlighted the significance of LF preventive and control measures that can target its seasonal epidemics. These measures could include strategies that can reduce human contact with the rodent vector as well as raise sensitization and awareness about LF among local residents especially those residing along the LF belt in eastern Sierra Leone.

Background: The study assessed the intention to accept a future COVID-19 vaccine in Nigeria and associated factors. Materials and Methods: Between July 2020 and August 2020, a cross-sectional study was conducted using an online questionnaire that captured demographic data, risk perception, trust in government and public health authorities and willingness to accept a future COVID-19 vaccine. Data were analyzed using Statistical Package for Social Science version 21.0, Chi-square and logistic regression were carried out at a 95% confidence interval. Appropriate institutional ethical board approval and informed consent were obtained from all participants. Results: 1,228 responses were received over the study period. The mean age of respondents was 32.8 years (SD 10.4), 12.7% (156/1,228) were health workers, 66.9% (820/1,228) had tertiary level of education. Intention to accept a future COVID-19 vaccine was expressed by 50.2% (617/1,228) of respondents. Increasing age, male gender, trust in government, trust in public health authorities, confidence in vaccine developers, willingness to pay for and travel for a vaccine, and vaccination during an outbreak were significantly associated with COVID-19 vaccine acceptance. Healthcare workers and respondents with pre-existing medical conditions were not significantly different from non-healthcare workers and persons without medical conditions respectively with regards to the willingness to be vaccinated. Conclusion: One in two persons would accept a COVID-19 vaccine when it becomes available in the country. The government should take pro-active steps to address the factors that may potentially impact on the benefits expected from the introduction of COVID-19 vaccine and scale-up vaccine sensitization to improve potential acceptance for uptake across the country.