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

Impact of Sleep Fragmentation on Cognition and Fatigue

Sleep continuity and efficacy are essential for optimal cognitive functions. How sleep fragmentation (SF) impairs cognitive functioning, and especially cognitive fatigue (CF), remains elusive. We investigated the impact of induced SF on CF through the TloadDback task, measuring interindividual variability in working memory capacity. Sixteen participants underwent an adaptation polysomnography night and three consecutive nights, once in a SF condition induced by non-awakening auditory stimulations, once under restorative sleep (RS) condition, counterbalanced within-subject. In both conditions, participants were administered memory, vigilance, inhibition and verbal fluency testing, and for CF the TloadDback, as well as sleep questionnaires and fatigue and sleepiness visual analog scales were administered. Subjective fatigue increased and sleep architecture was altered after SF (reduced sleep efficiency, percentage of N3 and REM, number of NREM and REM phases) despite similar total sleep time. At the behavioral level, only inhibition deteriorated after SF, and CF similarly evolved in RS and SF conditions. In line with prior research, we show that SF disrupts sleep architecture and exerts a deleterious impact on subjective fatigue and inhibition. However, young healthy participants appear able to compensate for CF induced by three consecutive SF nights. Further studies should investigate SF effects in extended and/or pathological disruption settings.info:eu-repo/semantics/publishe

Reversible Verbal Memory Integration Deficits in Obstructive Sleep Apnoea.

When presented with novel but semantically related elements after learning verbal material, healthy participants tend to endorse these items as previously learned. This reflects the normal integration and association of novel verbal information into long-term memory. How obstructive sleep apnoea (OSA) negatively impacts verbal memory performance, and whether deficits are reversible following positive airway pressure (PAP) treatment, remain elusive. We investigated immediate and delayed OSA- and PAP treatment-related effects on verbal memory integration, using a false memory paradigm. Twenty-three patients with OSA learned lists of words semantically related to target non-presented words (1) at baseline after a polysomnography diagnosis night, (2) after a consecutive polysomnography night under PAP titration, and (3) after three months of compliant PAP treatment. At each session, participants learned 10 different lists of words, each list comprising 15 semantically related items. They had then to recognize 15 minutes later (after an intermediate vigilance task) previously learned words within a list including studied words (learned), unstudied but semantically related items (lures), and non-related unstudied items (controls). Sleep quality and fatigue questionnaires, and psychomotor vigilance tests (PVT) were administered at each session. PAP treatment led to OSA remission and improvement in objective and subjective sleep quality. Crucially, recognition of learned and lure words increased after the first night under treatment and remained stable three months later, suggesting successful memory integration and restoration of semantic processes. No treatment-related outcome was found on PVT performance. OSA exerts a detrimental but PAP-reversible effect on verbal learning and semantic memory integration mechanisms underlying the acquisition of novel memory representations.info:eu-repo/semantics/publishe

Home confinement during the COVID-19: day-to-day associations of sleep quality with rumination, psychotic-like experiences, and somatic symptoms

info:eu-repo/semantics/publishe

Nights and days during the COVID-19 pandemic: a two weeks study on day-to-day associations between subjective sleep quality and mental complaints

info:eu-repo/semantics/publishe

Home confinement during the COVID-19: day-to-day associations of sleep quality with rumination, psychotic-like experiences, and somatic symptoms

info:eu-repo/semantics/nonPublishe

Home confinement during the COVID-19: day-to-day associations of sleep quality with rumination, psychotic-like experiences, and somatic symptoms

Due to the COVID-19 pandemic, populations from many countries have been confined at home for extended periods of time in stressful environmental and media conditions. Cross-sectional studies already evidence deleterious psychological consequences, with poor sleep as a risk factor for impaired mental health. However, limitations of cross-sectional assessments are response bias tendencies, and the inability to track daily fluctuations in specific subjective experiences in extended confinement conditions. In a prospective study conducted across three European countries, we queried participants (N = 166) twice a day through an online interface about their sleep quality and their negative psychological experiences for two consecutive weeks. Focus was set on between-and within-person associations of subjective sleep quality with daytime experiences such as rumination, psychotic-like experiences, and somatic complaints about the typical symptoms of the coronavirus. Results show that daily reports of country-specific COVID-19 deaths predicted increased negative mood, psychotic-like experiences and somatic complaints during the same day, and decreased subjective sleep quality the following night. Disrupted sleep was globally associated with negative psychological outcomes during the study period, and a relatively poorer night of sleep predicted increased rumination, psychotic-like experiences, and somatic complaints the following day. This temporal association was not paralleled by daytime mental complaints predicting relatively poorer sleep quality on the following night. Our findings show that night-to-night changes in sleep quality predict how individuals cope the next day with daily challenges induced by home confinement.info:eu-repo/semantics/publishe

Prevalence of Insomnia and Sleep Habits during the First and Second Wave of COVID-19 in Belgium

Belgium has one of the highest numbers of COVID-19 cases per 1 million inhabitants. The pandemic has led to significant societal changes with repercussions on sleep and on mental health. We aimed to investigate the effect of the first and the second wave of COVID-19 on the sleep of the Belgian populationWe launched two online questionnaires, one during the first lockdown (7240 respondents) and one during the second (3240 respondents), to test differences in self-reported clinical insomnia (as measured by the Insomnia Severity Index) and sleep habits during the two lockdowns in comparison with the pre-COVID period. The number of persons with clinical insomnia rose during the first lockdown (19.22%) and further during the second (28.91%) in comparison with pre-lockdown (7.04–7.66%). Bed and rise times were delayed and there was an increased time in bed and sleep onset latency. There was further a decrease in total sleep time and in sleep efficiency during both confinements. The prevalence of clinical insomnia quadrupled during the second wave in comparison with the pre-lockdown situation. Sleep habits were most altered in the younger population, indicating a greater risk for this group to develop a sleep-wake rhythm disorder