A cross-sectional study of malaria transmission in suggests the existence of a potential bridge vector susceptible of ensuring the transfer of simian malaria parasites to humans

Introduction: Despite all the efforts made to control or even eliminate malaria, the disease continues to claim the highest number of victims of vector-borne pathogens in the world and Sub-Saharan countries bear the heaviest burden. The lack of knowledge of the role of various protagonists involved in the transmission of this parasitic disease, such as mosquito vectors and the plasmodial species they transmit as well as the host species they infect in a locality, constitutes one of the main causes of the persistence of malaria. In Gabon, in several areas, entomological data on malaria transmission remain poorly known. Thus, this study aimed to determine the diversity of Anopheles involved in malaria transmission in different environments of the province of Nyanga in southwest Gabon.Methods: For this, an entomological study was carried out in the four main localities of the province of Nyanga to provide answers to these shortcomings. Mosquitoes were collected over several nights using the human landing catch method. The identification of Anopheles and malaria parasites circulating in the different sites was achieved by combining morphological and molecular analysis tools.Results: A total of five hundred and ninety-one (591) mosquitoes belonging to the Culicidae family were collected. From this collection of adult mosquitoes, nine species of Anopheles mosquitoes notably species of the Anopheles nili complex (53.46%) followed by those of Anopheles gambiae complex (22.01%), Anopheles funestus group (18.24%), Anopheles moucheti complex (5.66%) and Anopheles hancocki (0.63%). Approximately 18 percent of these Anopheles species were infected with Plasmodium spp. Anopheles funestus, known to be involved in malaria transmission to humans, and An. moucheti-like, recently discovered in Gabon, and whose status in Plasmodium transmission is not yet elucidated, were found to be infected with great ape Plasmodium.Discussion: Our results raise the question of the potential switch of simian malaria parasites to humans. If these observations are confirmed in the future, and the infective capacity of the bridge vectors is demonstrated, this new situation could ultimately constitute an obstacle to progress in the fight against malaria

Prevalence, genetic diversity and antiretroviral drugs resistance-associated mutations among untreated HIV-1-infected pregnant women in Gabon, central Africa

BACKGROUND: In Africa, the wide genetic diversity of HIV has resulted in emergence of new strains, rapid spread of this virus in sub-Saharan populations and therefore spread of the HIV epidemic throughout the continent. METHODS: To determine the prevalence of antibodies to HIV among a high-risk population in Gabon, 1098 and 2916 samples were collected from pregnant women in 2005 and 2008, respectively. HIV genotypes were evaluated in 107 HIV-1-positive samples to determine the circulating subtypes of strains and their resistance to antiretroviral drugs (ARVs). RESULTS: The seroprevalences were 6.3% in 2005 and 6.0% in 2008. The main subtype was recombinant CRF02_AG (46.7%), followed by the subtypes A (19.6%), G (10.3%), F (4.7%), H (1.9%) and D (0.9%) and the complex recombinants CRF06_cpx (1.9%) and CRF11_cpx (1.9%); 12.1% of subtypes could not be characterized. Analysis of ARVs resistance to the protease and reverse transcriptase coding regions showed mutations associated with extensive subtype polymorphism. In the present study, the HIV strains showed reduced susceptibility to ARVs (2.8%), particularly to protease inhibitors (1.9%) and nucleoside reverse transcriptase inhibitors (0.9%). CONCLUSIONS: The evolving genetic diversity of HIV calls for continuous monitoring of its molecular epidemiology in Gabon and in other central African countries

Retraction.

This is a retraction of 'Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa' 10.1126/science.add873

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

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

Viral etiology of influenza-like illness in adults and children and diarrheal syndrome in children in Gabon.

Les syndromes grippaux sont à l'origine des pathologies bénignes ou graves pouvant entrainer plusieurs millions de décès chaque année dans le monde. Ils s'expriment de façon épidémique, annuellement, et peuvent prendre un aspect pandémique. L'émergence d'une nouvelle souche de virus influenza A (pH1N1) en 2009 a suscité l'accroissement de la surveillance des virus grippaux. Par ailleurs, les syndromes diarrhéiques d'origine virale, représentent un problème majeur de santé publique chez les enfants de moins de 5 ans. Peu de données existent sur la circulation des virus grippaux et diarrhéiques au Gabon. Dans ce contexte, nous avons mis en place un réseau de surveillance des virus grippaux et diarrhéiques au Gabon. L'objectif de cette étude était de caractériser les virus responsables des syndromes grippaux et diarrhéiques dans quatre principales villes du Gabon. S'agissant des grippes, 1066 écouvillons nasaux ont été récoltés sur la période allant de Juillet 2009 à Juin 2011. Trois cent dix sept (317) selles ont été récoltées chez les enfants de moins de 5 ans dans la période allant de Mars 2010 à Juin 2011. Les étiologies virales ont été analysées par PCR en temps réel avec des amorces spécifiques des virus responsables des syndromes grippaux : les virus influenza A et B saisonnier, le virus influenza A pandémique (pH1N1), les parainfluenzavirus de type 1 à 4 (PIV1-4), le virus respiratoire syncytial (VRS), le métapneumovirus humain (hMPV), les coronavirus NL63 (HCoV-NL63), HKU1(HCoV-HKU1), OC43 (HCoV-OC43), 229E (HCoV-229E), les adénovirus (AdVs), les rhinovirus (HRVs), les parechovirus (HPeVs), les entérovirus (EVs). Les virus diarrhéiques recherchés ont été : les adénovirus, les norovirus de type 1 et 2 (NoV-I, NoV- II), les sapovirus (SaVs), les astrovirus (HAstVs) et les Rotavirus A (RVA). Les diversités génétiques ont été analysées par analyses phylogénétiques suivant les séquençages des fragments amplifiés. Parmi les écouvillons analysés, 61% (n=654) étaient positifs pour au moins un des virus recherchés : AdV (16%), PIVs (15%), virus influenza (13%), EV (12%), VRS (12%), HRV (8%), HCoVs (6,5%), hMPV (2%) et HPeV (0,5%). Les enfants de moins de cinq ans représentaient la population la plus susceptible (78%). Les co-infections virales ont été retrouvées dans près d'un tiers (1/3) des cas de syndromes grippaux : 25% (2 virus), 6% (3 virus) et 1 cas de co-infections par 4 virus. Elles concernent principalement les AdVs (41%) et EVs (43%). La saisonnalité des syndromes grippaux a été également mise en évidence : 70% surviennent pendant les saisons de pluies. La prévalence des étiologies virales des diarrhées chez les enfants de moins de 5 ans était de 60,9% (n=193). Les virus responsables de celles-ci étaient : RVA (21,7%), AdV (19,6%), NoV-I (9,1%), NoV-II (13,9%), SaV (9,5%) et HastV (6,3%). Parmi les AdV, le sérotype majoritaire était AdV-41 (espèce F) alors que le génotype majoritaire des astrovirus était HAstV-1. Nous avons obtenu un génotypage en G/P total ou partiel pour 59 patients. Les souches identifiées étaient : G1P[8] (8,5%), G2P[4] (3,4%), G3P[6] (1,7%), G6P[6] (40,7%), G12P[8] (3,4%), G1 (1,7%), G2 (3,4%), G3 (3,4%), G6 (13,5%), G12 (6,7%), P[6] (8,5%), P[8] (5,1%). Ce travail a permis la mise en place d'un réseau de surveillance des virus responsables des syndromes grippaux afin de mieux faire face aux épidémies et pandémies au Gabon. L'étude des syndromes diarrhéiques a permis d'identifier les souches circulant au Gabon, notamment celles de rotavirus ayant un impact en santé publique. Ces résultats permettent d'envisager une meilleure adaptation de la prise en charge thérapeutique et une réflexion en ce qui concerne la mise en place d'une stratégie vaccinale contre les rotavirus et les virus grippaux.Influenza-like illness (ILI) is causing mild to severe illnesses that can cause million of deaths each year worldwide. They cause epidemics annually or pandemics. The emergence of a new strain of influenza A virus (pH1N1) in 2009 sparked increased surveillance of influenza viruses. In addition, diarrheal syndromes represent a major public health problem among children under 5 years old. Few data exist on the circulation of influenza and diarrhea viruses in Gabon. In this context, a network surveillance of ILI and diarrhea virus was established in Gabon. The objective of this study was to characterize the viruses responsible of influenza-like illness and diarrhea in four major cities of Gabon.1066 nasal swabs were collected from July 2009 to June 2011. Three hundred and seventeen (317) stools were collected from children under 5 years old from March 2010 to June 2011. Viral etiologies were analyzed by real-time PCR with primers specifics of viruses responsible of ILI: seasonal influenza A and B, pandemic influenza, parainfluenza viruses type 1-4 (PIV1-4), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), coronaviruses NL63 (HCoV-NL63), HKU1 (HCoV-HKU1), OC43 (HCoV-OC43), 229E (HCoV-229E), adenoviruses (AdVs), rhinoviruses (HRVs), parechovirus (HPeVs), enteroviruses (EVs). The enteric viruses were: adenoviruses, noroviruses type 1, 2 (NoV-I, NoV- II), sapoviruses (SaVs), astroviruses (HAstVs) and rotaviruses A (RVA). Genetic diversity was analyzed by phylogenetic analysis following the sequencing of the amplified fragments.Among the swabs analyzed, 61% (n = 654) were positive for at least one virus: AdV (16%), PIVs (15%), virus influenza (13%), EV (12%), RSV (12%), HRV (8%), HCoVs (6.5%), hMPV (2%) and HPeV (0,5%). Children under five years old were the most susceptible population (78%). Viral co-infections were found in nearly one-third (1/3) cases of influenza-like illness: 25% (2 viruses), 6% (3 viruses) and 1 case of co-infection with four viruses. They mainly concerned AdV (41%) and EVs (43%). The seasonality of influenza-like illness has also been showed: 70% occured during the rainy seasons. The prevalence of viral etiologies of diarrhea in children under 5 years old was 60.9% (n = 193). The virus responsible of these were: RVA (21.7%), AdV (19.6%), NoV-I (9.1%), NoV-II (13.9%), SaV (9.5 %) and HastV (6.3%). Among the AdV, the majority serotype was AdV-41 (species F), while the majority of astrovirus genotype was HAstV-1. We got a total or partial genotyping G/P for 59 patients. The strains were identified: G1P[8] (8.5%), G2P[4] (3.4%), G3P[6] (1.7%), G6P[6] (40.7%), G12P[8] (3.4%), G1 (1.7%), G2 (3.4%), G3 (3.4%), G6 (13.5%), G12 (6.7%), P[6] (8.5%), P[8] (5.1%). This work allowed the establishment of a surveillance network of viruses responsible of ILI and diarrhea in order to deal with epidemics and pandemics in Gabon. The study of diarrheal syndromes identified strains circulating in Gabon, including rotavirus affecting public health. These results allow us to consider a better adaptation of therapeutic and reflection regarding the implementation of a vaccination strategy against rotavirus and influenza viruses

Detection of human bocavirus-1 in both nasal and stool specimens from children under 5 years old with influenza-like illnesses or diarrhea in Gabon

Abstract Objective Human bocavirus (HBoV) is a viral pathogen which causes respiratory tract diseases and acute gastroenteritis worldwide. This virus mainly affected children under 5 years old. There is little information on HBoV in Gabon. Two first studies was conducted to determine the prevalence of respiratory and enteric viruses in children under 5 years old who visited health centers for influenza-like illness (ILI) or diarrhea in Gabon from March 2010 to June 2011. However, HBoV was not included in the screening. The aim of this retrospective study was to evaluate the prevalence and the HBoV genotype in children under 5 years old with ILI or diarrhea in Gabon. Results A total of 810 nasal swabs and 317 feces samples collected during the two first study were analyzed among which 32 (4.4%) and 7 (2.2%) were positive for HBoV respectively. While there were no significant differences in prevalence between age groups in children with ILI, all children with diarrhea were under 12 months of age. Moreover, 84.4 and 42.8% were diagnosed in co-infections with at least one other respiratory virus, or enteric viruses respectively. Finally, HBoV subtype 1 has been detected in both respiratory and gastrointestinal tracts with very low variability