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

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

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

Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection

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

New Insights into Prevalence, Genetic Diversity, and Proviral Load of Human T-Cell Leukemia Virus Types 1 and 2 in Pregnant Women in Gabon in Equatorial Central Africa ▿

Human T-cell leukemia virus type 1 (HTLV-1) is highly endemic in areas of central Africa; mother-to-child transmission and sexual transmission are considered to be the predominant routes. To determine the prevalence and subtypes of HTLV-1/2 in pregnant women in Gabon, we conducted an epidemiological survey in the five main cities of the country. In 907 samples, the HTLV-1 seroprevalence was 2.1%, which is lower than that previously reported. Only one case of HTLV-2 infection was found. The HTLV-1 seroprevalence increased with age and differed between regions (P ≤ 0.05), with the highest prevalence (5%) in the southeastern region. A wide range of HTLV-1 proviral loads was observed among the infected women. The level of the proviral load was correlated with a high HTLV-1 antibody titer (P ≤ 0.02). Sequencing of HTLV-1 env and long terminal repeat fragments showed that all but one strain belonged to the central African subtype B; the outlier was of cosmopolitan subtype A. The new strains of subtype B exhibited wide genetic diversity, but there was no evidence of clustering of specific genomes within geographical regions of the country. Some strains were closely related to simian T-cell leukemia virus type 1 strains of great apes, suggesting that in these areas some HTLV-1 strains could arise from relatively recent interspecies transmission. The sole HTLV-2 strain belonged to subtype B. In this study we showed that the prevalence of HTLV-1 in the southeast is one of the highest in the world for pregnant women

Epidemiology and molecular characterization of the re-emerging measles virus among children and adults in the Haut-Ogooue, Gabon

Abstract Background Measles is one of the most infectious diseases with a high mortality rate worldwide. It is caused by the measles virus (MeV) which is a single stranded RNA virus with genetic diversity based on the nucleoprotein gene, including 24 genotypes. In Gabon, several outbreaks occurred in the past few years, especially in 2016 in Libreville and Oyem. A surveillance network of infectious diseases highlighted a measles outbreak which occurred in the south of Gabon from April to June 2017. Methods Clinical specimens of urine, blood, throat and nasal swabs were collected in the two main cities of the Haut-Ogooue province, Franceville and Moanda. Virological investigations based on real-time polymerase chain reaction for molecular diagnosis and conventional PCR for genotype identification were done. Results Specimens were collected from 139 suspected measles patients. A total of 46 (33.1%) children and adults were laboratory-confirmed cases among which 16 (34.8%) were unvaccinated, 16 (34.8%) had received one dose, and 11 (23.9%) had received two doses of the measles vaccine. Phylogenetic analysis revealed that all the sequences of the nucleoprotein gene belonged to genotype B3. Conclusions Measles infection was more commonly confirmed among those with one recorded dose compared to suspect cases with none, unknown or two recorded doses. The molecular characterization of the strains showed the circulation of the B3 genotype which is endemic on the African continent, thirty years after the B2 genotype was described in an outbreak in Libreville, the capital of Gabon. These findings highlight that surveillance and molecular investigation of measles should be continued in Gabon

A Sanger approach based on overlapping fragments to screen SARS-CoV-2 variants

Since the beginning of the COVID-19 pandemic, the SARS-CoV-2 virus has undergone various genetic mutations which have led to the emergence of variants. The World Health Organization (WHO) defines Variants of Concern (VOCs) and Variants of Interest (VOIs) according to several criteria. These include significant changes in the transmissibility and pathogenicity of the virus characterized by mutations in the spike gene coding the spike glycoprotein. In this study, we designed ten Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) assays in order to identify mutations of SARS-CoV-2 in overlapping fragments. Each assay contained mutations on the fragments sequenced by a Sanger method. The genomic analysis of the fragments allowed to identify the variant according to the position of the mutations. The assembly of the 10 fragments refined the analysis, highlighting all the mutations present in the S gene. Finally, a comparison of methods using a Next-Generation Sequencing (NGS) approches for samples enabled the method to be validated. By this method we have highlighted a characteristic mutation of the lineage B of SARS-CoV-2. We showed the circulation of SARS-CoV-2 belonging to lineage A and B in the beginning of the pandemic in Gabon. We have identified the Alpha, Delta and Omicron variants. This method would allow laboratories with limited financial means or without NGS instrument to obtain sequences of the S gene. This method wase very effective to highlight the circulation of variants, in particular VOCs and VOIs, in this developing country, Gabon, during the COVID-19 pandemic

Molecular epidemiology of enteric viruses and genotyping of rotavirus A, adenovirus and astrovirus among children under 5 years old in Gabon

Objectives: This study aimed to determine the prevalence of enteric viruses causing gastroenteritis, and the circulating stains, in Gabonese children under five years old who visited health centers between March 2010 and June 2011. Methods: Stool specimens were collected and sent for analysis to CIRMF (Centre International de Recherches Médicales de Franceville). Stools were screened for six enteric viruses (rotavirus, adenovirus, norovirus I and II, sapovirus, human astrovirus) by means of a multiplex real-time reverse transcription polymerase chain reaction, and Rotavirus A, Adenovirus and Astrovirus were genotyped. Results: Among the 317 specimens analyzed, 193 (60.9%) were positive for at least one enteric virus. Rotavirus A (RVA) (27.1%) was the most frequently detected virus, followed by human Adenovirus (HAdV) (19.6%), Norovirus II (NoVs-II) (13.9%), Norovirus I (NoVs-I) (9.1%), Sapovirus (SaV) (9.5%) and human Astrovirus (HAstV) (6.3%). One-third of the 193 positive samples contained more than one virus. The most common Rotavirus A genotype was G6P[6]. Various HAdV serotypes were found. HAstV-1 was identified. Conclusions: These findings improve our knowledge of circulating enteric viruses in Gabon. The emergence of unusual G6P[6] strain of rotavirus A, predominant, suggested a particular epidemiological surveillance of circulating rotavirus strains during the introduction of vaccination in Gabon