Baobab Index

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.

COVID-19 disease caused by SARS-CoV-2 represents an ongoing global public health emergency. Rapid identification of emergence, evolution, and spread of SARS-CoV-2 variants of concern (VOC) would enable timely and tailored responses by public health decision-making bodies. Yet, global disparities in current SARS-CoV-2 genomic surveillance activities reveal serious geographical gaps. Here, we discuss the experiences and lessons learned from the SARS-CoV-2 monitoring and surveillance program at the Public Health Laboratory on Bioko Island, Equatorial Guinea that was implemented as part of the national COVID-19 response and monitoring activities. We report how three distinct SARS-CoV-2 variants have dominated the epidemiological situation in Equatorial Guinea since March 2020. In addition, a case of co-infection of two SARS-CoV-2 VOC, Beta and Delta, in a clinically asymptomatic and fully COVID-19 vaccinated man living in Equatorial Guinea is presented. To our knowledge, this is the first report of a person co-infected with Beta and Delta VOC globally. Rapid identification of co-infections is relevant since these might provide an opportunity for genetic recombination resulting in emergence of novel SARS-CoV-2 lineages with enhanced transmission or immune evasion potential.

Malaria, a devastating febrile illness caused by protozoan parasites, sickened 247,000,000 people in 2021 and killed 619,000, mostly children and pregnant women in sub-Saharan Africa. A highly effective vaccine is urgently needed, especially for Sporozoites (SPZ), the parasite stage transmitted by First generation (radiation-attenuated) PfSPZ vaccines are safe, well tolerated, 80-100% efficacious against homologous controlled human malaria infection (CHMI) and provide 18-19 months protection without boosting in Africa. Second generation chemo-attenuated PfSPZ are more potent, 100% efficacious against stringent heterologous (variant strain) CHMI, but require a co-administered drug, raising safety concerns. Third generation, late liver stage-arresting, replication competent (LARC), genetically-attenuated PfSPZ are expected to be both safe and highly efficacious. Overall, PfSPZ vaccines meet safety, tolerability, and efficacy requirements for protecting pregnant women and travelers exposed to Pf in Africa, with licensure for these populations possible within 5 years. Protecting children and mass vaccination programs to block transmission and eliminate malaria are long-term objectives. Introduction Malaria, a devastating febrile illness caused by protozoan parasites, sickened 247,000,000 people in 2021 and killed 619,000, mostly children and pregnant women in sub-Saharan Africa. A highly effective vaccine is urgently needed, especially for Plasmodium falciparum (Pf), the deadliest human malaria parasite. Areas covered Sporozoites (SPZ), the parasite stage transmitted by Anopheles mosquitoes to humans, are the only vaccine immunogen achieving >90% efficacy against Pf infection. This review describes >30 clinical trials of PfSPZ vaccines in the U.S.A., Europe, Africa, and Asia, based on first-hand knowledge of the trials and PubMed searches of ‘sporozoites,’ ‘malaria,’ and ‘vaccines.’ Expert opinion First generation (radiation-attenuated) PfSPZ vaccines are safe, well tolerated, 80–100% efficacious against homologous controlled human malaria infection (CHMI) and provide 18–19 months protection without boosting in Africa. Second generation chemo-attenuated PfSPZ are more potent, 100% efficacious against stringent heterologous (variant strain) CHMI, but require a co-administered drug, raising safety concerns. Third generation, late liver stage-arresting, replication competent (LARC), genetically-attenuated PfSPZ are expected to be both safe and highly efficacious. Overall, PfSPZ vaccines meet safety, tolerability, and efficacy requirements for protecting pregnant women and travelers exposed to Pf in Africa, with licensure for these populations possible within 5 years. Protecting children and mass vaccination programs to block transmission and eliminate malaria are long-term objectives.

Pfhrp2 and pfhrp3 deletions are threatening Plasmodium falciparum malaria diagnosis by rapid diagnostic tests (RDT) due to false negatives. This study assesses the changes in the frequencies of pfhrp2 and pfhrp3 deletions (pfhrp2 A total of 566 P. falciparum samples were genotyped to assess the presence of pfhrp2 and pfhrp3 deletions and their flanking genes. The specimens were collected 18 years apart from two provinces of Equatorial Guinea, North Bioko (Insular Region) and Litoral Province (Continental Region). Orthologs of pfhrp2 and pfhrp3 genes from other closely related species were used to compare sequencing data to assess pfhrp2 and pfhrp3 evolution. Additionally, population structure was studied using seven neutral microsatellites. This study found that pfhrp2Del and pfhrp3Del were present before the introduction of RDT; however, they increased in frequency after their use, reaching more than 15%. Haplotype networks suggested that pfhrp2Del and pfhrp3Del emerged multiple times. Exon 2 of pfhrp2 and pfhrp3 genes had high variability, but there were no significant changes in amino acid sequences. Baseline sampling before deploying interventions provides a valuable context to interpret changes in genetic markers linked to their efficacy, such as the dynamic of deletions affecting RDT efficacy.

Effective malaria control requires accurate identification of Plasmodium infections to tailor interventions appropriately. Rapid diagnostic tests (RDTs) are crucial tools for this purpose due to their small size and ease-of-use functionality. These tests typically target the Plasmodium falciparum histidine-rich protein 2 (HRP2) antigen. However, some strains of P. falciparum have deletions in the hrp2 and hrp3 genes, which may result in a false negative diagnosis using HRP2-based RDTs. Additionally, RDTs have a detection limit of 100 parasites per microlitre, insufficient for identifying low-density infections that sustain malaria transmission. This study explores integrating molecular monitoring using a novel cartridge-based PCR test, PlasmoPod, using samples from a malaria indicator survey (MIS) on Bioko Island, Equatorial Guinea to enhance detection of low-density infections and inform targeted malaria control strategies. The study utilized a combination of RDTs and the DiaxxoPCR device for molecular monitoring. The device DiaxxoPCR uses a prefilled cartridge system, termed PlasmoPod for a malaria-based assay that employs a qPCR assay targeting 18S rDNA/rRNA. Samples from the 2023 MIS were extracted from dried blood spots (DBS), qPCR run in duplicate on the PlasmoPod. Epidemiological data from the MIS were merged with molecular data and the association between MIS variables to malaria infection by qPCR, and low-density infections were measured. The integration of molecular monitoring revealed a proportion of low-density infections that circumvented RDTs diagnosis. Notably, individuals in urban communities and those reporting recent fever were more likely to harbour low-density, asymptomatic malaria infections. Findings suggest that urban residents, although less associated to malaria infection than rural residents by both RDT and qPCR, may be serving as a transmission reservoir. The relationship between low-density infections and individuals who recently reported fever may reflect recent anti-malarial treatment or natural clearance, and thus have lingering parasites in their blood. The study highlights the limitations of HRP2-based RDTs in detecting low density infections and underscores the potential of molecular tools like PlasmoPod in malaria surveillance. By identifying elusive transmission reservoirs and tracking parasite importation, molecular monitoring can play a crucial role in achieving malaria elimination. The findings advocate for the broader implementation of molecular diagnostics in malaria programs, especially in areas with low transmission, to enhance the detection and targeting of hidden reservoirs of infection.

Recent surveys in the Congolian rainforest have significantly improved the quantity and quality of material available to rigorously assess bat diversity (Order Chiroptera) in this biodiversity hotspot. However, the paucity of data on free-tailed bats in this region is hindering our ability to resolve the actual number of species present in Central Africa. During a recent expedition to continental Equatorial Guinea, a single free-tailed bat was captured in a patch of primary continental rainforest. This bat exhibited unique external and cranial characteristics, strongly suggesting it to be a male of

The Bioko Island Malaria Elimination Project (BIMEP) has made significant progress in reducing the prevalence of Plasmodium falciparum on Bioko Island, Equatorial Guinea. However, like other malaria endemic islands like São Tomé and Principe and Zanzibar, Tanzania, elimination efforts are hampered by imported infections. In an effort to understand the local transmission dynamics and the influence of importation on Bioko Island's P. falciparum population, whole-genome sequences were generated from field samples collected during the BIMEP's 2019 Malaria Indicator Survey (MIS). Within the sub-Saharan African context, we observed Bioko Island parasites did not significantly differentiate from nearby continental neighbors. Among Bioko infections, within-host diversity and the quantity of polyclonal infections appear similar to an area of moderate malaria transmission. However, we observed higher than expected genetic diversity among Bioko parasites, similar to high transmission areas, suggesting imported strains are contributing to transmission on the island. Among Bioko's closest geographical neighbors, the flow of parasites with Bioko appeared more pronounced with the Gabonese parasite population, implying more importation may be coming from this region than others. Overall, despite significant investment in malaria control, results illustrate the challenges of eliminating malaria without both interrupting local transmission and accounting for importation from higher transmission areas, likely due to human migration. For there to be sustained progress towards elimination, the BIMEP needs, if feasible, to conduct targeted interventions of outgoing/incoming travelers, expand malaria control interventions to the continental region of Equatorial Guinea, and ideally conduct cross-border interventions in collaboration with the malaria control program in Gabon.

Developmental disorders (DD), including intellectual disability (ID) and birth defects, affect approximately 7% of individuals worldwide, contributing to high mortality and lifelong morbidity. These disorders impose significant financial and psychological burdens on affected families. Genetic causes are identified in over 40% of DD cases, but diagnostic challenges, lack of appropriate management and curative treatments, and limited knowledge of natural history complicate management. Genetic testing, such as exome sequencing, is the standard diagnostic approach in developed countries. However, access to genetics services in low- and middle-income countries remains limited. Key barriers include poor access to specialist services in general, limited infrastructure, insufficient expertise in medical genetics, and outdated medical training curricula. The Deciphering Developmental Disorders in Africa (DDD-Africa) international training program initiative aims to address some of these disparities by establishing a network of trained professionals across African countries. This network will drive genomic research by identifying patients with DD, assessing them appropriately to direct genomic testing, and providing support to affected families. The training program consists of three phases: (1) an online course covering training in current core medical genetics concepts, (2) a 2-week on-site practical training in Johannesburg in identification, clinical assessment, and variant interpretation of DD patients, and (3) a hands-on implementation of the complete diagnostic process with four families recruited at each team's home institute. The program trains healthcare professionals consisting of a clinician and laboratory scientist together, emphasizing the need for collaboration and a comprehensive understanding of integrated genetic clinical assessment and laboratory diagnostics. Ultimately, the initiative seeks to enhance diagnostic capabilities and family support, fostering a strong pan-African network in the field of DD.

Chickenpox is a highly contagious viral infection caused by varicella-zoster virus (VZV) whose clinical manifestations mimic mpox posing challenges for diagnosis without laboratory confirmation. Here, we investigated VZV among the mpox-suspected cases, May to October 2022, in Ethiopia. Samples were collected from 202 mpox-suspected cases in 11 of Ethiopia's 14 regions and screened for mpox virus by real-time polymerase chain reaction (RT-PCR). Then, differential testing of other selected orthopoxviruses, VZV and herpes simplex virus (HSV) were conducted for 133 randomly selected samples. Whole-genome sequencing (WGS) and downstream analysis was performed on 8 VZV-positive samples. Descriptive statistics were used to summarize epidemiological and clinical data. All the 202 enrolled cases tested negative for mpox. Of these, 133 samples were tested for VZV, and 107 (80.5%, 95% CI: 72.9% - 86.3%) turned positive but remained negative for HSV and other tested orthopoxviruses. At least one VZV-positive case was reported in each region sampled. Half (49.6%) of the cases were hospitalized, with no fatalities. The sequences were clustered primarily in Clade 5 (62.5%, 5) followed by Clade 3 (25.0%, 2) and Clade 1 (12.5%, 1). This investigation confirmed VZV as the predominant causative agent among mpox-suspected cases. To our knowledge, this represents the first clade-level genomic characterization of VZV from Ethiopia, revealing circulation of multiple clades among samples collected during May to October 2022. The findings highlight the need to strengthen differential diagnostic capacities including multiplex testing, and building genomic surveillance capacities for epidemic intelligence and outbreak response.