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

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

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

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

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

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

Reduced Cancer Incidence in Huntington's Disease: Analysis in the Registry Study

Background: People with Huntington's disease (HD) have been observed to have lower rates of cancers. Objective: To investigate the relationship between age of onset of HD, CAG repeat length, and cancer diagnosis. Methods: Data were obtained from the European Huntington's disease network REGISTRY study for 6540 subjects. Population cancer incidence was ascertained from the GLOBOCAN database to obtain standardised incidence ratios of cancers in the REGISTRY subjects. Results: 173/6528 HD REGISTRY subjects had had a cancer diagnosis. The age-standardised incidence rate of all cancers in the REGISTRY HD population was 0.26 (CI 0.22-0.30). Individual cancers showed a lower age-standardised incidence rate compared with the control population with prostate and colorectal cancers showing the lowest rates. There was no effect of CAG length on the likelihood of cancer, but a cancer diagnosis within the last year was associated with a greatly increased rate of HD onset (Hazard Ratio 18.94, p < 0.001). Conclusions: Cancer is less common than expected in the HD population, confirming previous reports. However, this does not appear to be related to CAG length in HTT. A recent diagnosis of cancer increases the risk of HD onset at any age, likely due to increased investigation following a cancer diagnosis

Clinical and genetic characteristics of late-onset Huntington's disease

Background: The frequency of late-onset Huntington's disease (&gt;59 years) is assumed to be low and the clinical course milder. However, previous literature on late-onset disease is scarce and inconclusive. Objective: Our aim is to study clinical characteristics of late-onset compared to common-onset HD patients in a large cohort of HD patients from the Registry database. Methods: Participants with late- and common-onset (30–50 years)were compared for first clinical symptoms, disease progression, CAG repeat size and family history. Participants with a missing CAG repeat size, a repeat size of ≤35 or a UHDRS motor score of ≤5 were excluded. Results: Of 6007 eligible participants, 687 had late-onset (11.4%) and 3216 (53.5%) common-onset HD. Late-onset (n = 577) had significantly more gait and balance problems as first symptom compared to common-onset (n = 2408) (P &lt;.001). Overall motor and cognitive performance (P &lt;.001) were worse, however only disease motor progression was slower (coefficient, −0.58; SE 0.16; P &lt;.001) compared to the common-onset group. Repeat size was significantly lower in the late-onset (n = 40.8; SD 1.6) compared to common-onset (n = 44.4; SD 2.8) (P &lt;.001). Fewer late-onset patients (n = 451) had a positive family history compared to common-onset (n = 2940) (P &lt;.001). Conclusions: Late-onset patients present more frequently with gait and balance problems as first symptom, and disease progression is not milder compared to common-onset HD patients apart from motor progression. The family history is likely to be negative, which might make diagnosing HD more difficult in this population. However, the balance and gait problems might be helpful in diagnosing HD in elderly patients