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

Blastocystis sp. Infection: Prevalence and Clinical Aspects among Patients Attending to the Laboratory of Parasitology–Mycology of Fann University Hospital, Dakar, Senegal

Introduction: Blastocystis sp. is a unicellular obligate anaerobic protozoa found in the human intestinal tract. Its role in human health is widely discussed because of the high proportion of asymptomatic carriers. In sub-Saharan Africa, the prevalence of the disease is underestimated. This study was performed to describe the epidemiological, clinical, and parasitological aspects of Blastocystis sp. infection in patients attending to Fann University Hospital. Material and Methods: We carried out a retrospective and descriptive study among patients attending to the laboratory of Parasitology and Mycology of Fann University Hospital from January 2016 to December 2020. All stool samples collected were examined using direct examination, a formal ether concentration method, and a modified Zeilh–Nielsen staining method. A descriptive analysis was performed with Stata MP 16 software. The significance level was set at 5%. Results: Overall, 447 cases of Blastocystis sp. were reported in our study, representing a prevalence rate of 13.7% ((447/3264) (95% CI: 12.5–15.5)). The mean age of the patients was 26 ± 20.7 years. Subjects over 45 years of age were more affected, with a frequency of 14.7%. Blastocystis sp. carriage was more common in males, at 14.6%. The symptomatology was mainly represented by diarrhea, abdominal pain, and dyspeptic disorders. In asymptomatic patients, the frequency of Blastocystis sp. was 33.3%. Mono-infection was found in 78.6% of cases. In total, 96 patients were carriers of at least two parasites (21.5%). Blastocystis sp. was most associated with Entamoeba coli (8.1%) and Endolimax nanus (4.03%). The association with helminths was noted in 5 patients (3 Ascaris lumbricoides, Trichuris trichiura, and Taenia). Conclusion: These results show the frequency of Blastocystis sp. infection with a large proportion of asymptomatic carriers. The presence of the parasite in the stool, associated with digestive disorders or with the association of other intestinal parasites, could justify the initiation of an anti-parasitic treatment

Epidemiological and Mycological Aspects of Onychomycosis in Dakar (Senegal)

Onychomycosis is a fungal nails infection often caused by yeasts, dermatophytes and molds. It is an important public health concern due to its high prevalence, the problem of diagnostics, and the poor response to treatments. The objective of this study was to evaluate the epidemiological and microbiological profile of onychomycosis diagnosed at the Laboratory of Parasitology-Mycology of the National University Hospital of Fann in Dakar, Senegal, from 2012 to 2016. A retrospective and descriptive study was performed from January 2012 to December 2016 in a patient attending the laboratory of Parasitology-Mycology at the Fann teaching hospital. Socio-demographic, clinical and biological data were collected from the bench registers. Samples from the lesions were tested using direct microscopy and cultured on a Sabouraud-Chloramphenicol and Sabouraud-Chloramphenicol-Actidione medium. A descriptive analysis was done using Stata IC 12 software. The significance level of different tests was set at 5% two-side. A total of 469 patients were included in this study. The mean age of the study population was 33.2 ± 15.2 years, and the sex ratio was 0.52. The prevalence of onychomycosis was 48.4% (227/469). The main clinical presentations were disto-lateral subungual onychomycosis (37.9%) and onyxis (46.5%). Identified fungal species were Candida albicans (42.7%), Candida spp. (39.5%), Trichophyton soudanense (10.1%), Fusarium spp. (5.3%), and Candida tropicalis (2.6%). Candida albicans was more frequent in subjects over 15 years of age (43.6%) and women (45%). However, Trichophyton soudanense was higher in patients under 15 years old (17.4%) as well as in male subjects (18.8%). In conclusion, onychomycosis is a common cause of consultation in health facilities. Candida albicans and Trichophyton Soudanense are the main fungal species causing onychomycosis. A better understanding of the epidemiology of onychomycosis as well as the spectrum of the pathogen could contribute to improve the management of the infection

A Study of Trichomonas vaginalis Infection and Correlates in Women with Vaginal Discharge Referred at Fann Teaching Hospital in Senegal

Introduction. Trichomoniasis is nowadays the most prevalent non-viral sexually transmitted infection in the world. In Senegal, the epidemiology of trichomoniasis is not well known. The current study aimed at assessing the prevalence and factors associated with T. vaginalis infection among women with vaginal discharge. Methods. A retrospective analysis of laboratory records from patients referred at the Fann Teaching Hospital in Dakar, Senegal, for vaginal discharge was carried out. The study covered the period from 2006 to 2011. For each participating woman, a vaginal swab was collected and a wet mount smear performed immediately. Optic microscopic examination with 40x magnification was done to detect T. vaginalis and assess biological modifications such as presence of epithelial cells, white blood cells, and red blood cells. A gram stained smear was also performed and examined under oil immersion (100x magnification) to assess the vaginal flora. Results. Overall, 3893 women were enrolled with a mean age at 31.2 ± 10 years. The prevalence of Trichomoniasis represented 4.8%, 95%CI(3.1-5.7) and it was lower among women less than 30 years (4.1%), while divorced women more likely to be infected compared to married and single women (aOR:2.1, 95%CI (1.2-3.7)). Trichomoniasis was associated with abnormal vaginal flora such as type III (aOR:2.6, 95%CI(1.5-4.4)) and type IV (aOR:3.3, 95%CI(2.1-5.3)). In addition, patients with erythrocytes excretion were more likely to be infected by T. vaginalis (aOR:2.8, 95%CI(1.9-3.9). Conclusion. Trichomonas vaginalis remains prevalent among sexually active women. Strategies aiming at improving disease awareness in these high-risk groups are needed to improve trichomoniasis prevention but extensive epidemiological data are still needed for a better understanding of the disease transmission dynamic

Sero-epidemiological evaluation of Plasmodium falciparum malaria in Senegal

BACKGROUND: In Senegal, a significant decrease of malaria transmission intensity has been noted the last years. Parasitaemia has become lower and, therefore, more difficult to detect by microscopy. In the context of submicroscopic parasitaemia, it has become relevant to rely on relevant malaria surveillance tools to better document malaria epidemiology in such settings. Serological markers have been proposed as an essential tool for malaria surveillance. This study aimed to evaluate the sero-epidemiological situation of Plasmodium falciparum malaria in two sentinel sites in Senegal. METHODS: Cross-sectional surveys were carried out in Velingara (south Senegal) and Keur Soce (central Senegal) between September and October 2010. Children under 10 years old, living in these areas, were enrolled using two-level, random sampling methods. P. falciparum infection was diagnosed using microscopy. P. falciparum antibodies against circumsporozoite protein (CSP), apical membrane protein (AMA1) and merozoite surface protein 1_42 (MSP1_42) were measured by ELISA method. A stepwise logistic regression analysis was done to assess factors associated with P. falciparum antibodies carriage. RESULTS: A total of 1,865 children under 10 years old were enrolled. The overall falciparum malaria prevalence was 4.99% with high prevalence in Velingara of 10.03% compared to Keur Soce of 0.3%. Symptomatic malaria cases (fever associated with parasitaemia) represented 17.37%. Seroprevalence of anti-AMA1, anti-MSP1_42 and anti-CSP antibody was 38.12, 41.55 and 40.38%, respectively. The seroprevalence was more important in Velingara and increased with age, active malaria infection and area of residence. CONCLUSION: The use of serological markers can contribute to improved malaria surveillance in areas with declining malaria transmission. This study provided useful baseline information about the sero-epidemiological situation of malaria in Senegal and can contribute to the identification of malaria hot spots in order to concentrate intervention efforts. TRIAL REGISTRATION NUMBER: PACTR201305000551876 ( http://www.pactr.org )