The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by ...that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata.
In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related.
The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.
Streptococcus pneumoniae (S. pneumoniae), remains a major cause of mortality and morbidity worldwide. The objective of this study was to determine the trends of invasive pneumococcal diseases (IPD) ...in adult and elderly population in Casablanca (Morocco) before and after introduction of pneumococcal conjugate vaccine (PCV) by determining the distribution of pneumococcal serotypes and antibiotic resistance profile of isolated strains.
The proposed study is a retrospective laboratory-based surveillance of IPD in hospitalized adult (15-59 years old) and elderly (≥ 60 years old) patients in Ibn Rochd University Hospital Centre from 2007 to 2019 (13 years). All the 250 non-duplicate clinical invasive isolates from adult and elderly patients, confirmed as S. pneumoniae according to the laboratory standard identification procedures, are included in this study.
A significant decrease of the overall incidence in IPD was observed only in adults from 0.71 to 0.54/100000 populations (P = 0.02) and to 0.47/100000 populations (P = 0.0137) in the early and mature post-vaccine period respectively compared to the pre-vaccine period. Our results also showed a significant reduction in the overall prevalence of vaccine serotypes from 28.17 to 6.90% (P = 0.0021) for the PCV-10 serotypes, and from 46.48 to 25.86% (P = 0.0164) for the PCV-13 serotypes only in the mature post-vaccine period (2015-2019). In parallel, the rate of non-vaccine serotypes did not significantly change in the early post-vaccine period (2011-2014) while it increased considerably from 54 to 74.14% (P = 0.0189) during the mature post-vaccine period. The rate of penicillin non-susceptible pneumococcal isolates decreased significantly from 23.94 to 8.77% (P = 0.02) in adult patients, and the rate of cotrimoxazole non-susceptible pneumococcal isolates significantly decreased from 29.58 to 8.77% in the early post-vaccine period (P = 0.003) and to 7.24% in the mature post-vaccine period (P = 0.0007).
Although childhood vaccination has considerably reduced the incidence of IPD in adult population through the herd effect, IPD remain a real public health problem due to the alarming increase in non-vaccine serotypes (NVS) and the lack of herd effect among elderly population. The rate of antibiotic resistance was relatively low. Nevertheless, resistance constitutes a serious problem to the therapeutic arsenal due to the known capacity for genetic dissemination in the pneumococcus.
Abstract 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.
Rapid diagnostic tests (RDTs) are a key tool for the diagnosis of malaria infections among clinical and subclinical individuals. Low-density infections, and deletions of the P. falciparum hrp2/3 ...genes (encoding the HRP2 and HRP3 proteins detected by many RDTs) present challenges for RDT-based diagnosis. The novel Rapigen Biocredit three-band Plasmodium falciparum HRP2/LDH RDT was evaluated among 444 clinical and 468 subclinical individuals in a high transmission setting in Burundi. Results were compared to the AccessBio CareStart HRP2 RDT, and qPCR with a sensitivity of <0.3 parasites/μL blood. Sensitivity compared to qPCR among clinical patients for the Biocredit RDT was 79.9% (250/313, either of HRP2/LDH positive), compared to 73.2% (229/313) for CareStart (P = 0.048). Specificity of the Biocredit was 82.4% compared to 96.2% for CareStart. Among subclinical infections, sensitivity was 72.3% (162/224) compared to 58.5% (131/224) for CareStart (P = 0.003), and reached 88.3% (53/60) in children <15 years. Specificity was 84.4% for the Biocredit and 93.4% for the CareStart RDT. No (0/362) hrp2 and 2/366 hrp3 deletions were observed. In conclusion, the novel RDT showed improved sensitivity for the diagnosis of P. falciparum.
Within the first 14 days after outbreak confirmation, the East African Community Mobile laboratory network was actively involved in providing Sudan virus disease and differential diagnostics in the ...epicentre at Mubende Regional Referral Hospital (and neighbouring districts), as well as in coordination of mobile laboratory preparedness activities in five other East African countries. Introduction On 20 September 2022, the Ugandan Ministry of Health declared an Ebola Sudan virus disease (SVD) outbreak in the Mubende District of the country, with one confirmed SVD death and six probable deaths reported in the region since 1 September 2022.1 Since 2017, and with funding from the German Federal Ministry for Economic Cooperation and Development through the KfW Development Bank, the East African Community (EAC) together with the Bernhard-Nocht-Institute for Tropical Medicine established a network of nine mobile EAC laboratories embedded within the National Public Health Laboratories (NPHLs) of six EAC Partner States (Tanzania, Kenya, Burundi, Rwanda, South Sudan and Uganda).2 3 These field-deployable mobile laboratories have the capacity to diagnose risk group four pathogens, such as SVD. On the same day of the SVD outbreak announcement (20 September 2022) by the Ugandan government, the EAC Health Department initiated their regional pandemic preparedness and response activities, which consisted of a two-pronged approach: while the mobilisation of the EAC mobile laboratory network commenced, the regional procurement of diagnostic kits for SVD and differential diagnosis was immediately initiated (for a detailed timeline of events, see table 1).Table 1 Timeline of regional SVD outbreak response and preparedness activities in six East African countries Days following outbreak announcement 1 2 3 4 5 6 7 8 9 10 11 12 13 14 SVD outbreak declared by Uganda MoH EAC secretariat Emergency pandemic preparedness meetings Emergency procurement initiated Logistical support (kit delivery) Technical country support Press Release No of SVD kits ordered/expected 1×96 tests (arrival day 20) Uganda SVD outbreak response Request for support to EAC Lab deployment from Kampala to Mubende Start of testing No of SVD kits ordered/received 4×96 tests No. Diagnostic workflows, standard operating procedures and supply of diagnostics kits The EAC Mobile laboratories consist of negative pressure gloveboxes (Könnecke, Germany) (see figure 2) for sample inactivation and Bio-Rad CFX96 RT-PCR platforms for molecular SVD diagnosis (for further details on the laboratory setup, see Affara et al2).
Background: The computerization of the health record is one of the means to improve the performance of the information system within the hospital and therefore improve the continuity and quality of ...care and services offered to the population. The objective of this work was to determine the factors associated with the satisfaction of providers with the hospital information system based on the electronic health record.Methods: This is a cross-sectional, descriptive and analytical study carried out in 11 hospitals in Burundi. A self-administered questionnaire was used to collect data from a sample of 155 providers. The data analysis was done with STATA 15.Results: The majority were nurses (51%) followed by physicians (23%). Regarding satisfaction, 55.5% of the providers were satisfied with the new EHR-based system. Men were 2.21 times more satisfied with the use of the EHR than women (OR=2.21; CI95%: 1.09-4.46). Providers who were trained by the project's computer scientists were 4.24 more satisfied than those who were trained by their colleagues (OR=4.24; CI95%: 1.47-12.23) and 3.69 more satisfied than those who were trained by the hospital's computer scientists (OR = 3.69; CI95%: 1.25-10.89). Similarly, the use of the software to generate reports and statistics was 2.27 times associated with provider satisfaction (OR=2.27; 95% CI: 1.14-4.49.Conclusions: The sustainability and success of the patient record computerization project depends on taking into account the expectations of the providers during the implementation.
BackgroundThe emergence of SARS-CoV-2 variants has significantly increased the number of cases of COVID-19 among vaccinated individuals, raising concerns about the effectiveness of current vaccines. ...The aim of this study was to analyze the SARS-CoV-2 infection risks after primary vaccination with BNT162b2, BBIBP-CorV, or ChAdOx1-nCOV-19 and after homologues and heterologous booster vaccinations with these vaccines, as well as the profiles of reinfected patients.MethodsWe analyzed retrospectively 1082 patients vaccinated or unvaccinated with BNT162b2, BBIBP-CorV, and/or ChAdOx1nCoV-19 vaccines to determine their SARS-CoV2 infection statuses using the reverse transcription-polymerase chain reaction (RT-PCR) in addition to their clinical features. The infection risks of patients receiving the different vaccine regimens were compared using multivariate logistic regression analysis, comparing the adjusted OR of a positive COVID-19 test result.ResultsAmong 596 vaccinated patients, 53%(n = 286) tested positive for SARS-CoV-2 and 57%(n = 310) tested negative. Among positive cases, 10 were reinfection cases. The risk of SARS-CoV-2 infection was 1.6 (adj. OR) for patients who received one dose compared with those who received two doses (95% CI = 1.3-1.8; p < 0.01).The risk was 2.6 (adj. OR) for patients who received one dose compared with those who received three doses (95%CI = 2.1-3.3; p < 0.01), and 1.6 (adj. OR) for patients who received two doses compared with those who received three doses (95% CI = 1.3-2; p < 0.01). The patients who received two doses that were heterologous to that of the primary vaccine had the lowest risk of infection. Booster vaccinations (third dose) significantly reduced the number of positive cases with an acceptable safety profile. Higher cycle-threshold (Ct) values (indicative of viral load) were observed in vaccinated patients, whereas low Ct values were observed in unvaccinated patients.ConclusionA complete cycle of vaccination with homologous vaccines or heterologous vaccines resulted in an acceptable reduction in SARS-CoV-2 infection. Further, vaccination was associated with a reduction in viral load.
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