Abstract The COVID-19 pandemic significantly accelerated the development of genomic surveillance capabilities worldwide, though equitable access remains a challenge. On 12 March 2020, Guinea, a low-income country in West Africa, reported its first COVID-19 case; however, no local genomic infrastructure was available at the time. A year later, a long-term training program program was initiated to establish a SARS-CoV-2 nanopore sequencing unit at the Centre de Recherche en Virologie, Laboratoire des Fièvres Hémorragiques Virales de Guinée (CRV-LFHVG) in Conakry, Guinea. Here, we describe the establishment of this capacity and its role in uncovering SARS-CoV-2 circulation dynamics in the region. We established a local hub for comprehensive sequencing training (wet-lab and bioinformatics), where SARS-CoV-2-positive samples, collected as part of routine diagnostic activities from July 2020 to July 2022, were retrospectively and prospectively sequenced using the ONT MinION device. Consensus genomes were generated for variant typing and GISAID-submission. Retrospective phylodynamic analysis was performed. By July 2022, the laboratory had generated 238 SARS-CoV-2 consensus sequences with a median genomic recovery of 98.1% [range: 90.5–99.4], representing 0.64% of the 37,464 confirmed cases reported in the country as of 29 July 2022. These sequences encompassed four waves of infection, with the Delta (21 A, 21I and 21 J) and Omicron (21 K and 21 L) variants of concern (VOCs) accounting for 84% of all identified lineages. Phylogeographic reconstructions revealed introductions of Delta/B.1.617.2 and Delta/AY.37, as well as of Omicron/BA.1.1 and Omicron/BA.1.15.1, potentially from the neighboring Western, Eastern and Middle African regions. Retrospective and prospective sequencing output was > 0.5% of the total positive samples and the results were communicated to the health authorities during the pandemic as in two preliminary variant identification reports, followed by six official reports. This work underscores key findings during a global health crisis and offers operational guidance to support future genomic surveillance initiatives in low- and middle-income countries. Sustained financial investment, dedicated time, specialized expertise, efficient logistics, and local ownership are essential for long-term implementation of such capacities.
Biomphalaria and Physa (order Gastropoda) serve as vectors and reservoirs for infectious agents that affect both humans and animals. This study provides updated insights into the epidemiology, morphology, phylogeny, and haplotype diversity of Biomphalaria and Physa snails in Guangdong Province, southern China. Field surveys were conducted across Guangdong Province from 2016 to 2023. Morphological observations included assessment of snail shape, shell height, and aperture width. Molecular analysis targeted several genes, including Cytochrome c oxidase subunit 1 (COI), internal transcribed spacer (ITS), 18S rRNA, 16S rRNA, and 28S rRNA. Evolutionary trees were constructed with neighbor-joining and maximum likelihood methods. Haplotype networks were generated from COI sequences collected from multiple geographic locations. Physa acuta was detected in 92
Introduction:Several arboviral diseases have been known to be endemic (e.g., Crimean-Congo hemorrhagic fever, Rift Valley fever) or are emerging (dengue fever, chikungunya, O'nyong-nyong) in human populations in Mauritania, while others have become rare in recent years (e.g. yellow fever). Moreover, domestic animals, especially cattle, camels, goats, and sheep, are also known to be infected with some of these arboviruses (e.g. Crimean-Congo hemorrhagic fever, Rift Valley fever). For these reasons, viral hemorrhagic fever surveillance in Mauritania is part of the Integrated Disease Surveillance and Response (IDSR). However, limited information is available on the efficacy of the viral hemorrhagic fever surveillance system in the Assaba region of Mauritania. The aim of the present study was to assess the performance of the surveillance system, in particular its general utility, simplicity, flexibility, acceptability, and reactivity. Methods:A descriptive cross-sectional study was conducted from July to August 2022 in the Assaba region with the objective of evaluating the characteristics of the system by interviewing key actors involved in the surveillance of viral hemorrhagic fevers, with a focus on Rift Valley fever and Crimean-Congo hemorrhagic fever, using questionnaires developed following the guidelines of the Centers for Disease Control and Prevention (Atlanta, Georgia, USA). Data from 2020-2022 on viral hemorrhagic fevers from the National Institute of Public Health laboratory were analyzed. Medians, interquartile ranges, and proportions were calculated using Epi Info® 7.2.5.0 and Excel® 2021. Results:The questionnaire was answered by all twenty-six persons involved in the viral hemorrhagic fever surveillance system in Assaba region. The majority of survey respondents found the system to be useful (51%), simple (63%), acceptable (46%), responsive (64%), and flexible (46%). An analysis of the data revealed a positive predictive value of 28% for Rift Valley Fever. The weekly distribution of cases within the wilaya indicates that the moughataa of Kiffa recorded the highest number of cases in September, with a notable weekly peak during that month in 2020. According to the analysis of the National Institute of Public Health database, cases of viral hemorrhagic fevers were promptly handled. Survey responses and database analysis revealed issues related to data quality and data management mechanisms. These limitations in the surveillance system are likely to be due to insufficient resources and training of the personnel, in particular with regards to data collection and management, which in turn led to incomplete or missing data and invalid data entry. These weak points can be ascribed, at least in part, to financial constraints and inadequate attribution of priority to arboviral diseases. Despite these limitations, disease data generated by the surveillance system were generally reliable. Conclusion:The viral hemorrhagic fever surveillance system in the Assaba region adheres to the organization and functioning of the national viral hemorrhagic fever surveillance system, which is part of the IDSR. The characteristics of utility, simplicity, responsiveness, and flexibility of the viral hemorrhagic fever surveillance system are good, but acceptability and flexibility need further improvement. The earlier the first arboviral human or animal cases are detected, the more likely an active intervention can be organized in response to the emerging epidemic or epizootic and prevent the spread of the disease. An efficient viral surveillance system is the key to reducing the negative impact of arboviral diseases in Assaba region.
We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.
Background A third of people living with HIV (PLHIV) in Western Africa had an undiagnosed infection in 2020. In 2019-2021, the ATLAS programme has distributed a total of 380 000 HIV self-testing (HIVST) kits to key populations (KP) including female sex workers (FSW) and men who have sex with men (MSM), and their partners in Côte d’Ivoire, Mali and Senegal. We predicted the potential impact of ATLAS and of national HIVST scale-up strategies among KP. Methods A deterministic model of HIV transmission was calibrated to country-specific empirical HIV and intervention data over time. We simulated scenarios reflecting 1) the actual ATLAS HIVST distribution only over 2019-2021 (∼2% of all tests done in countries), and 2) ATLAS followed by a scale-up of HIVST distribution to KP (total of ∼570 000 kits distributed each year). Impacts on HIV diagnosis, new HIV infections and deaths were derived using counterfactual scenarios without HIVST. Findings ATLAS was predicted to substantially increase HIV diagnosis among KP by the end of 2021, especially among MSM in Mali (9·3 percentage point [pp] increase), and a 1·0pp increase overall. ATLAS might have averted a median of 706 new HIV infections among KP over 2019-2028 in the 3 countries combined, especially among MSM, and 1794 new HIV infections (0·4-3·3% of all new HIV infections across countries) and 591 HIV-related deaths overall. HIVST scale-up increased HIV diagnosis at the end of 2028 by around 8pp among FSW and 33pp among MSM in every country. Overall increases ranged from 1·0pp (Côte d’Ivoire) to 11·0pp (Senegal). HIVST scale-up may avert 3-5% of new HIV infections among FSW, 3-10% among FSW clients, and 20-28% among MSM across countries (and 2-16% overall), and avert 13-18% of HIV-related deaths among MSM over 2019-2028. Interpretation Scaling-up HIVST distribution among KP in Western Africa may substantially attenuate disparities in access to HIV testing and help reduce HIV infections and deaths among KP and their partners. Funding Unitaid MRC ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by Unitaid (Grant Number: 2018-23 ATLAS) through a collaborative agreement with Solthis. RS and MCB acknowledge funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union. PV, MCB and MMG acknowledge funding from the Wellcome Trust (WT 226619/Z/22/Z). MMG research program is supported Tier 2 Canada Research Chairs. For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) license to any Author Accepted Manuscript version arising. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors
