19 research outputs found

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

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    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

    Adult mosquito predation and potential impact on the sterile insect technique

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    International audienceThe sterile insect technique is a promising environmentally friendly method for mosquito control. This technique involves releasing laboratory-produced sterile males into a target field site, and its effectiveness may be affected by the extent of adult mosquito predation. Sterile males undergo several treatments. Therefore, it is vital to understand which treatments are essential in minimizing risks to predation once released. The present study investigates the predation propensity of four mantis species ( Phyllocrania paradoxa, Hymenopus coronatus, Blepharopsis mendica, Deroplatys desiccata ) and two gecko species ( Phelsuma standingi, P. laticauda) on adult Aedes aegypti , Ae. albopictus and Anopheles arabiensis mosquitoes in a laboratory setting. First, any inherent predation preferences regarding mosquito species and sex were evaluated. Subsequently, the effects of chilling, marking, and irradiation, on predation rates were assessed. The selected predators effectively preyed on all mosquito species regardless of the treatment. Predation propensity varied over days for the same individuals and between predator individuals. Overall, there was no impact of laboratory treatments of sterile males on the relative risk of predation by the test predators, unless purposely exposed to double the required sterilizing irradiation dose. Further investigations on standardized predation trials may lead to additional quality control tools for irradiated mosquitoes

    : J Public Health Afr

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    Little is known on the impact of HIV-2 infection on HCV viral replication. The aim of the study was to compare HCV prevalence and viral replication based on HIV types in West Africa. A cross-sectional survey was conducted within the IeDEA HIV-2 West Africa cohort from March to December 2012. All HIVinfected adult patients who attended participating HIV clinics during the study period were included. Blood samples were collected and re-tested for HIV type discrimination, HCV serology and viral load. A total of 767 patients were enrolled: 186 HIV-1, 431 HIV-2 and 150 HIV-1&2 dually reactive. At time of sampling, 531 (69.2%) were on ART and median CD4+ cell count was 472/mm(3). Thirty (3.9%, 95% CI 2.7-5.5) patients were anti-HCV positive (4.3% in HIV-1, 4.0% in HIV-1&2 dually reactive and 3.7% in HIV-2; p=0.91). Detectable HCV RNA was identified in 21 (70.0%) patients (100% in HIV-1 and HIV- 1&2 dually reactive vs. 43.8% in HIV-2; p=0.003). Systematic screening should be promoted and performed in this population, since HCV is now potentially curable in sub- Saharan Africa

    Semi-field and indoor setups to study malaria mosquito swarming behavior

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    International audienceBackground: The recent resurgence of interest in sterile insect techniques to control vector mosquitoes has renewed interest in novel methods for observing mating behavior. Malarial vectors of the Anopheles gambiae complex are known to mate in swarms at specific locations at dawn and dusk. Most knowledge of mosquito swarming behavior is derived from field observations and a few experimental studies designed to assess critical parameters that affect mosquito swarming. However, such studies are difficult to implement in the field because of uncontrollable environmental factors and mosquito conditions. Here, we present two experimental setups specifically designed to analyze mosquito swarming behavior and provide evidence that swarming behavior of mosquitoes can be generated and accurately assessed under both semi-field and laboratory conditions.Methods: The Mosquito Ecology Research Facility setup is a semi-field enclosure made of 12 compartments (10.0 × 6.0 × 4.5 m L × W × H each) exposed to ambient meteorological and lighting conditions. The laboratory setup consists of a windowless room (5.1 × 4.7 × 3.0 m) in which both environmental and mosquito conditions can be controlled. In the two setups, 300 3-6-days-old An. coluzzii virgin males were released and some swarm characteristics were recorded such as the time at which the swarm started, the number of mosquitoes in the swarm and the height. Climatic conditions in the semi-field setup were also recorded.Results: In both setups, An. coluzzii males displayed stereotyped and consistent swarming behavior day after day; males gradually gather into a swarm over a ground marker at sunset, flying in loops in relation to specific visual features on the ground. Although semi-field climatic conditions were slightly different from outdoors conditions, they did not impede swarming behavior and swarm characteristics were similar to those observed in the field.Conclusions: Swarm characteristics and their consistency across days provide evidences that these facilities can be used confidently to study swarming behavior. These facilities come to complement existing semi-field setups and pave the way for new experimental studies which will enhance our understanding of mating behavior but also mosquito ecology and evolution, a prerequisite for application of genetic approaches to malaria control

    Pilot study on the combination of an organophosphate-based insecticide paint and pyrethroid-treated long lasting nets against pyrethroid resistant malaria vectors in Burkina Faso

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    International audienceA pilot study to test the efficacy of combining an organophosphate-based insecticide paint and pyrethroid-treated Long Lasting Insecticide Treated Nets (LLINs) against pyrethroid-resistant malaria vector mosquitoes was performed in a real village setting in Burkina Faso. Paint Inesfly 5A IGR™, comprised of two organophosphates (OPs) and an Insect Growth Regulator (IGR), was tested in combination with pyrethroid-treated LLINs. Efficacy was assessed in terms of mortality for 12 months using Early Morning Collections of malaria vectors and 30-minute WHO bioassays. Resistance to pyrethroids and OPs was assessed by detecting the frequency of L1014F and L1014S kdr mutations and Ace-1(R)G119S mutation, respectively. Blood meal origin was identified using a direct enzyme-linked immunosorbent assay (ELISA). The combination of Inesfly 5A IGR™ and LLINs was effective in killing 99.9-100% of malaria vector populations for 6 months regardless of the dose and volume treated. After 12 months, mortality rates decreased to 69.5-82.2%. The highest mortality rates observed in houses treated with 2 layers of insecticide paint and a larger volume. WHO bioassays supported these results: mortalities were 98.8-100% for 6 months and decreased after 12 months to 81.7-97.0%. Mortality rates in control houses with LLINs were low. Collected malaria vectors consisted exclusively of Anopheles coluzzii and were resistant to pyrethroids, with a L1014 kdr mutation frequency ranging from 60 to 98% through the study. About 58% of An. coluzzii collected inside houses had bloodfed on non-human animals. Combining Inesfly 5A IGR™ and LLINs yielded a one year killing efficacy against An. coluzzii highly resistant to pyrethroids but susceptible to OPs that exhibited an anthropo-zoophilic behaviour in the study area. The results obtained in a real setting supported previous work performed in experimental huts and underscore the need to study the impact that this novel strategy may have on clinical malaria and malaria exposure in children in a similar area of high pyrethroid resistance in South-Western Burkina Faso

    Impact of irradiation on the reproductive traits of field and laboratory An. arabiensis mosquitoes

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    Abstract Background The sterile insect technique (SIT) aims at suppressing or decreasing insect pest populations by introducing sterile insects into wild populations. SIT requires the mass-production of insects and their sterilization through, for example, radiation. However, both mass-rearing and radiation can affect the life history traits of insects making them less competitive than their wild counterparts. In the malaria mosquito Anopheles arabiensis, some progress has been made to improve the mating competitiveness of mass-reared irradiated males. However, to date, no study has explored the relative effects of colonization and irradiation on important reproductive traits in this species. Such data may help to focus research efforts more precisely to improve current techniques. Methods Two strains of An. arabiensis originating from the same locality were used: one reared in the laboratory for five generations and the second collected as late larval instars in the field prior to experimentation. Pupae were irradiated with 95 Gy and some adult reproductive traits, including insemination rate, fecundity, oviposition behavior, fertility and male survivorship, were assessed in different mating combinations. Results Our study revealed the different effects of mosquito strain and irradiation on reproductive processes. The insemination rate was higher in field (67.3%) than in laboratory (54.9%) females and was negatively affected by both female and male irradiation (un-irradiated vs irradiated: 70.2 vs 51.3% in females; 67.7 vs 53.7% in males). Irradiated females did not produce eggs and egg prevalence was lower in the field strain (75.4%) than in the laboratory strain (83.9%). The hatching rate was higher in the field strain (88.7%) than in the laboratory strain (70.6%) as well as in un-irradiated mosquitoes (96.5%) than in irradiated ones (49%). Larval viability was higher in the field strain (96.2%) than in the laboratory strain (78.5%) and in un-irradiated mosquitoes (97.6%) than irradiated ones (52%). Finally, field males lived longer than laboratory males (25.1 vs 20.5 days, respectively). Conclusions Our results revealed that both irradiation and colonization alter reproductive traits. However, different developmental stages are not equally affected. It is necessary to consider as many fitness traits as possible to evaluate the efficacy of the sterile insect technique

    Targeted application of an organophosphate-based paint applied on windows and doors against Anopheles coluzzii resistant to pyrethroids under real life conditions in Vallée du Kou, Burkina Faso (West Africa)

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    International audienceBackground: A novel strategy applying an organophosphate-based insecticide paint on doors and windows in combination with long-lasting insecticide-treated nets (LLINs) was tested for the control of pyrethroid-resistant malaria vectors in a village setting in Vallée du Kou, a rice-growing area west of Burkina Faso.Methods: Insecticide Paint Inesfly 5A IGR ™ , comprised of two organophosphates and an insect growth regulator, was applied to doors and windows and tested in combination with pyrethroid-treated LLINs. The killing effect was monitored for 5 months by early morning collections of anophelines and other culicids. The residual efficacy was evaluated monthly by WHO bioassays using Anopheles gambiae 'Kisumu' and local populations of Anopheles coluzzii resistant to pyrethroids. The spatial mortality efficacy (SME) at distances of 1 m was also assessed against pyrethroid-susceptible and-resistant malaria vectors. The frequency of L1014F kdr and Ace-1 R G119S mutations was, respectively , reported throughout the study. The Insecticide Paint Inesfly 5A IGR had been tested in past studies yielding a long-term mortality rate of 80% over 12 months against An. coluzzii, the local pyrethroid-resistant malaria vector. The purpose of the present study is to test if treating smaller, targeted surfaces (e.g. doors and windows) was also efficient in killing malaria vectors.Results: Treating windows and doors alone yielded a killing efficacy of 100% for 1 month against An. coluzzii resistant to pyrethroids, but efficacy reduced quickly afterwards. Likewise, WHO cone bioassays yielded mortalities of 80-100% for 2 months but declined to 90 and 40% 2 and 3 months after treatment, respectively. Mosquitoes exposed to insecticide paint-treated surfaces at distances of 1 m, yielded mortality rates of about 90-80% against local pyrethroids-resistant An. coluzzii during the first 2 months, but decreased to 30% afterwards. Anopheles coluzzii was reported to be exclusively the local malaria vector and resistant to pyrethroids with high L1014 kdr frequency

    Effect of irradiation on the survival and susceptibility of female Anopheles arabiensis to natural isolates of Plasmodium falciparum

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    International audienceBackground: The sterile insect technique (SIT) is a vector control strategy relying on the mass release of sterile males into wild vector populations. Current sex separation techniques are not fully efficient and could lead to the release of a small proportion of females. It is therefore important to evaluate the effect of irradiation on the ability of released females to transmit pathogens. This study aimed to assess the effect of irradiation on the survival and competence of Anopheles arabiensis females for Plasmodium falciparum in laboratory conditions.Methods: Pupae were irradiated at 95 Gy of gamma-rays, and emerging females were challenged with one of 14 natural isolates of P. falciparum. Seven days post-blood meal (dpbm), irradiated and unirradiated-control females were dissected to assess the presence of oocysts, using 8 parasite isolates. On 14 dpbm, sporozoite dissemination in the head/thorax was also examined, using 10 parasites isolates including 4 in common with the 7 dpbm dissection (oocyst data). The survivorship of irradiated and unirradiated-control mosquitoes was monitored.Results: Overall, irradiation reduced the proportion of mosquitoes infected with the oocyst stages by 17% but this effect was highly inconsistent among parasite isolates. Secondly, there was no significant effect of irradiation on the number of developing oocysts. Thirdly, there was no significant difference in both the sporozoite infection rate and load between the irradiated and unirradiated-control mosquitoes. Fourthly, irradiation had varying effects on female survival with either a negative effect or no effect.Conclusions: The effect of irradiation on mosquito competence strongly varied among parasite isolates. Because of such isolate variability and, the fact that different parasite isolates were used to collect oocyst and sporozoite data, the irradiation-mediated reduction of oocyst prevalence was not confirmed for the sporozoite stages. Our data indicate that irradiated female An. arabiensis could contribute to malaria transmission, and highlight the need for perfect sex-ing tools, which would prevent the release of females as part of SIT programmes
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