Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community.

The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% (n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC's NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.

Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.

COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.

The national burden of influenza-associated severe acute respiratory illness hospitalization in Rwanda, 2012-2014.

BACKGROUND: Estimates of influenza-associated hospitalization are severely limited in low- and middle-income countries, especially in Africa. OBJECTIVES: To estimate the national number of influenza-associated severe acute respiratory illness (SARI) hospitalization in Rwanda. METHODS: We multiplied the influenza virus detection rate from influenza surveillance conducted at 6 sentinel hospitals by the national number of respiratory hospitalization obtained from passive surveillance after adjusting for underreporting and reclassification of any respiratory hospitalizations as SARI during 2012-2014. The population at risk was obtained from projections of the 2012 census. Bootstrapping was used for the calculation of confidence intervals (CI) to account for the uncertainty associated with all levels of adjustment. Rates were expressed per 100 000 population. A sensitivity analysis using a different estimation approach was also conducted. RESULTS: SARI cases accounted for 70.6% (9759/13 813) of respiratory admissions at selected hospitals: 77.2% (6783/8786) and 59.2% (2976/5028) among individuals aged <5 and ≥5 years, respectively. Overall, among SARI cases tested, the influenza virus detection rate was 6.3% (190/3022): 5.7% (127/2220) and 7.8% (63/802) among individuals aged <5 and ≥5 years, respectively. The estimated mean annual national number of influenza-associated SARI hospitalizations was 3663 (95% CI: 2930-4395-rate: 34.7; 95% CI: 25.4-47.7): 2637 (95% CI: 2110-3164-rate: 168.7; 95% CI: 135.0-202.4) among children aged <5 years and 1026 (95% CI: 821-1231-rate: 11.3; 95% CI: 9.0-13.6) among individuals aged ≥5 years. The estimates obtained from both approaches were not statistically different (overlapping CIs). CONCLUSIONS: The burden of influenza-associated SARI hospitalizations was substantial and was highest among children aged <5 years.