Bringing the social into vaccination research: Community-led ethnography and trust-building in immunization programs in Sierra Leone

Background Vaccine hesitancy is a complex, contested social phenomenon and existing research highlights the multifaceted role of trust in strengthening vaccine confidence. However, understanding public engagement with vaccination through the lens of (mis)trust requires more contextual evidence on trust's qualitative determinants. This includes expanding the geographic focus beyond current studies' focus on High Income Countries. Furthermore, obstacles remain in effectively integrating social science findings in the design of vaccine deployment strategies, and in ensuring that those who implement interventions and are affected by them are directly involved in producing knowledge about vaccination challenges. Methods We piloted a community-led ethnographic approach, training Community Health Workers (CHWs) in Kambia District, Sierra Leone, in qualitative social science methods. Methods included participant observation, participatory power mapping and rumour tracking, focus group discussions and key stakeholder interviews. CHWs, with the support of public health officials and professional social scientists, conducted research on vaccination challenges, analysed data, tested new community engagement strategies based on their findings and elicited local perspectives on these approaches. Results Our findings on vaccine confidence in five border communities highlighted three key themes: the impact of prior experiences with the health system on (mis)trust; relevance of livelihood strategies and power dynamics for vaccine uptake and access; and the contextual nature of knowledge around vaccines. Across these themes, we show how expressions of trust centered on social proximity, reliability and respect and the role of structural issues affecting both vaccine access and confidence. The pilot also highlighted the value and practical challenges to meaningfully co-designed research. Conclusion There is scope for broader application of a community-led ethnographic approach will help redesign programming that is responsive to local knowledge and experience. Involving communities and low-cadre service providers in generating knowledge and solutions can strengthen relationships and sustain dialogue to bolster vaccine confidence

An Update on the Surveillance of Livestock Diseases and Antimicrobial Use in Sierra Leone in 2021-An Operational Research Study.

In Sierra Leone, in 2020, a study by the Livestock and Veterinary Services Division (Ministry of Agriculture and Forestry) on the surveillance system of animal diseases and antimicrobial use found poor reporting. Of the expected weekly districts reports, <1% were received and only three of the 15 districts had submitted reports occasionally between 2016 and 2019. Following this, staff-capacity-building on reporting was undertaken. In 2021, we reassessed the improvement in reporting and used the reports to describe livestock diseases and antimicrobials utilized in their treatment. Between March and October 2021, 88% of expected weekly reports from all 15 districts were received. There were minor deficiencies in completeness and consistency in the terminology used for reporting animal disease and antimicrobials. Available reports showed that 25% of the livestock had an infectious disease, and a quarter of the sick animals had received an antimicrobial drug. Most animals received antimicrobials belonging to World Organization for Animal Health's "veterinary critically important" category (77%) and World Health Organization's "critically" (17%) and "highly important" (60%) categories for human health. These indicate a significant improvement in the animal health surveillance system and highlight the need for enhanced antimicrobial stewardship to prevent misuse of antimicrobials that are significant in animal and human health

Isolation of Angola-like Marburg virus from Egyptian rousette bats from West Africa.

Marburg virus (MARV) causes sporadic outbreaks of severe Marburg virus disease (MVD). Most MVD outbreaks originated in East Africa and field studies in East Africa, South Africa, Zambia, and Gabon identified the Egyptian rousette bat (ERB; Rousettus aegyptiacus) as a natural reservoir. However, the largest recorded MVD outbreak with the highest case-fatality ratio happened in 2005 in Angola, where direct spillover from bats was not  shown. Here, collaborative studies by the Centers for Disease Control and Prevention, Njala University, University of California, Davis USAID-PREDICT, and the University of Makeni identify MARV circulating in ERBs in Sierra Leone. PCR, antibody and virus isolation data from 1755 bats of 42 species shows active MARV infection in approximately 2.5% of ERBs. Phylogenetic analysis identifies MARVs that are similar to the Angola strain. These results provide evidence of MARV circulation in West Africa and demonstrate the value of pathogen surveillance to identify previously undetected threats

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Improvement in the Surveillance System for Livestock Diseases and Antimicrobial Use Following Operational Research Studies in Sierra Leone January–March 2023

In Sierra Leone, two operational research (OR) studies in 2019 and 2021 showed deficiencies in the data being captured by the Integrated Animal Disease Surveillance and Reporting (IADSR) system. This third OR study was conducted in 2023 to assess whether the second OR study’s results and recommendations were disseminated with the key stakeholders, the uptake of the recommendations, improvements in data capture in the IADSR system, and to describe the data on livestock disease and antimicrobial use. In 2022, on seven occasions, the authors of the second OR study disseminated the study’s findings. Of the four recommendations, the one on improving laboratory infrastructure for confirmation of animal disease was not implemented. The district animal health weekly surveillance reports received through the IADSR system were sustained at 88% between the second (2021) and third (2023) studies. In both studies, the proportion of sick animals receiving antibiotics (25%) remained the same, but the use of “critically important antimicrobials for veterinary use” declined from 77% (in 2021) to 69% (in 2023). The IADSR system has improved considerably in providing information on animal health and antibiotic use, and sequential OR studies have played a key role in its improvement

Isolation of Angola-like Marburg virus from Egyptian rousette bats from West Africa.

Marburg virus (MARV) causes sporadic outbreaks of severe Marburg virus disease (MVD). Most MVD outbreaks originated in East Africa and field studies in East Africa, South Africa, Zambia, and Gabon identified the Egyptian rousette bat (ERB; Rousettus aegyptiacus) as a natural reservoir. However, the largest recorded MVD outbreak with the highest case-fatality ratio happened in 2005 in Angola, where direct spillover from bats was not  shown. Here, collaborative studies by the Centers for Disease Control and Prevention, Njala University, University of California, Davis USAID-PREDICT, and the University of Makeni identify MARV circulating in ERBs in Sierra Leone. PCR, antibody and virus isolation data from 1755 bats of 42 species shows active MARV infection in approximately 2.5% of ERBs. Phylogenetic analysis identifies MARVs that are similar to the Angola strain. These results provide evidence of MARV circulation in West Africa and demonstrate the value of pathogen surveillance to identify previously undetected threats