RESUMO
In December 2023, we observed through hospital-based surveillance a severe outbreak of enterovirus D68 infection in pediatric inpatients in Dakar, Senegal. Molecular characterization revealed that subclade B3, the dominant lineage in outbreaks worldwide, was responsible for the outbreak. Enhanced surveillance in inpatient settings, including among patients with neurologic illnesses, is needed.
Assuntos
Surtos de Doenças , Enterovirus Humano D , Infecções por Enterovirus , Infecções Respiratórias , Humanos , Senegal/epidemiologia , Enterovirus Humano D/genética , Enterovirus Humano D/classificação , Enterovirus Humano D/isolamento & purificação , Infecções por Enterovirus/epidemiologia , Infecções por Enterovirus/virologia , Infecções por Enterovirus/diagnóstico , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/virologia , Pré-Escolar , Lactente , Criança , Filogenia , Masculino , Feminino , Doença Aguda/epidemiologia , Adolescente , Hospitais , História do Século XXIRESUMO
Despite decades of influenza surveillance in many African countries, little is known about the evolutionary dynamics of seasonal influenza viruses. This study aimed to characterize the epidemiological, genetic and antigenic profiles of A/H3N2 viruses in Senegal from 2010 to 2022. A/H3N2 infection was confirmed using reverse transcription-polymerase chain reaction. Subsequently, a representative of A/H3N2 isolates was selected for genome sequencing. Predicted vaccine efficacy was measured using the Pepitope model. During the study period, 22638 samples were tested and influenza was detected in 31.8%, among which type A was confirmed in 78.1%. Of the Influenza A cases, the H3N2 subtype was detected in 29.8%, peaking at expected times during the rainy season. Genome sequencing of 123A/H3N2 isolates yielded 24 complete and 99 partial genomic sequences. Phylogenetic analysis revealed the circulation of multiple clades of A/H3N2 in Senegal, including 2a.3, 3C.2 and 3C.3a. A/H3N2 isolates were mainly susceptible to the influenza antiviral drugs oseltamivir and zanamivir, but the primary adamantine-resistance marker, S31N was encountered in all isolates. At least nine potential N-linked glycosylation sites were predicted among A/H3N2 strains, six of which (at positions 24, 38, 79, 181, 262 and 301) remains conserved among all isolates. Antigenic distances between circulating strains and vaccine viruses indicated varying vaccine efficacies, from suboptimal to moderate protection. The findings emphasize the need to enhance local genomic and antigenic surveillance and further research on influenza epidemiology and genetic evolution in sub-Saharan Africa.
Assuntos
Antígenos Virais , Vírus da Influenza A Subtipo H3N2 , Influenza Humana , Filogenia , Senegal/epidemiologia , Humanos , Influenza Humana/epidemiologia , Influenza Humana/virologia , Vírus da Influenza A Subtipo H3N2/genética , Vírus da Influenza A Subtipo H3N2/imunologia , Vírus da Influenza A Subtipo H3N2/isolamento & purificação , Vírus da Influenza A Subtipo H3N2/classificação , Adulto , Antígenos Virais/genética , Antígenos Virais/imunologia , Adulto Jovem , Pré-Escolar , Feminino , Pessoa de Meia-Idade , Adolescente , Masculino , Criança , Idoso , Antivirais/uso terapêutico , Lactente , Vacinas contra Influenza/imunologia , Monitoramento Epidemiológico , Genoma Viral , Estações do Ano , Farmacorresistência Viral/genética , Eficácia de Vacinas , Evolução Molecular , Idoso de 80 Anos ou maisRESUMO
Historically low levels of seasonal influenza circulation were reported during the first years of the COVID-19 pandemic and were mainly attributed to implementation of nonpharmaceutical interventions. In tropical regions, influenza's seasonality differs largely, and data on this topic are scarce. We analyzed data from Senegal's sentinel syndromic surveillance network before and after the start of the COVID-19 pandemic to assess changes in influenza circulation. We found that influenza shows year-round circulation in Senegal and has 2 distinct epidemic peaks: during January-March and during the rainy season in August-October. During 2021-2022, the expected January-March influenza peak completely disappeared, corresponding to periods of active SARS-CoV-2 circulation. We noted an unexpected influenza epidemic peak during May-July 2022. The observed reciprocal circulation of SARS-CoV-2 and influenza suggests that factors such as viral interference might be at play and should be further investigated in tropical settings.
Assuntos
COVID-19 , Influenza Humana , Humanos , COVID-19/epidemiologia , SARS-CoV-2 , Senegal/epidemiologia , Influenza Humana/epidemiologia , PandemiasRESUMO
Environmental surveillance for poliovirus is increasingly used in poliovirus eradication efforts as a supplement to acute flaccid paralysis (AFP) surveillance. Environmental surveillance was officially established in 2017 in Senegal, where no poliovirus had been detected since 2010. We tested sewage samples from 2 sites in Dakar monthly for polioviruses. We identified a vaccine-derived poliovirus serotype 2 on January 19, 2021, from a sample collected on December 24, 2020; by December 31, 2021, we had detected 70 vaccine-derived poliovirus serotype 2 isolates circulating in 7 of 14 regions in Senegal. Sources included 18 AFP cases, 20 direct contacts, 17 contacts in the community, and 15 sewage samples. Phylogenetic analysis revealed the circulation of 2 clusters and provided evidence on the virus introduction from Guinea. Because novel oral polio vaccine serotype 2 was used for response activities throughout Senegal, we recommend expanding environmental surveillance into other regions.
Assuntos
Poliomielite , Poliovirus , Humanos , Monitoramento Ambiental , Filogenia , Poliomielite/epidemiologia , Poliomielite/prevenção & controle , Poliovirus/genética , Vacina Antipólio Oral/efeitos adversos , Senegal/epidemiologia , Sorogrupo , EsgotosRESUMO
This overview of severe acute respiratory syndrome coronavirus 2 circulation over 1.5 years in Guinea demonstrates that virus clades and variants of interest and concern were progressively introduced, mostly by travellers through Conakry, before spreading through the country. Sequencing is key to following virus evolution and establishing efficient control strategies.
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COVID-19 , SARS-CoV-2 , Guiné/epidemiologia , HumanosRESUMO
In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay's clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.
Assuntos
COVID-19/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real/métodos , Recombinases/metabolismo , SARS-CoV-2/isolamento & purificação , COVID-19/virologia , Humanos , Sensibilidade e EspecificidadeRESUMO
BACKGROUND: Influenza is a major cause of morbidity and mortality in Africa. However, a lack of epidemiological data remains for this pathology, and the performances of the influenza-like illness (ILI) case definitions used for sentinel surveillance have never been evaluated in Senegal. This study aimed to i) assess the performance of three different ILI case definitions, adopted by the WHO, USA-CDC (CDC) and European-CDC (ECDC) and ii) identify clinical factors associated with a positive diagnosis for Influenza in order to develop an algorithm fitted for the Senegalese context. METHODS: All 657 patients with a febrile pathological episode (FPE) between January 2013 and December 2016 were followed in a cohort study in two rural villages in Senegal, accounting for 1653 FPE observations with nasopharyngeal sampling and influenza virus screening by rRT-PCR. For each FPE, general characteristics and clinical signs presented by patients were collected. Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) for the three ILI case definitions were assessed using PCR result as the reference test. Associations between clinical signs and influenza infection were analyzed using logistic regression with generalized estimating equations. Sore throat, arthralgia or myalgia were missing for children under 5 years. RESULTS: WHO, CDC and ECDC case definitions had similar sensitivity (81.0%; 95%CI: 77.0-85.0) and NPV (91.0%; 95%CI: 89.0-93.1) while the WHO and CDC ILI case definitions had the highest specificity (52.0%; 95%CI: 49.1-54.5) and PPV (32.0%; 95%CI: 30.0-35.0). These performances varied by age groups. In children < 5 years, the significant predictors of influenza virus infection were cough and nasal discharge. In patients from 5 years, cough, nasal discharge, sore throat and asthenia grade 3 best predicted influenza infection. The addition of "nasal discharge" as a symptom to the WHO case definition decreased sensitivity but increased specificity, particularly in the pediatric population. CONCLUSION: In summary, all three definitions studies (WHO, ECDC & CDC) have similar performance, even by age group. The revised WHO ILI definition could be chosen for surveillance purposes for its simplicity. Symptomatic predictors of influenza virus infection vary according the age group.
Assuntos
Influenza Humana/epidemiologia , Influenza Humana/etiologia , Adolescente , Adulto , Centers for Disease Control and Prevention, U.S. , Criança , Pré-Escolar , Estudos de Coortes , Tosse/etiologia , Tosse/virologia , Feminino , Febre/etiologia , Febre/virologia , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Faringite/complicações , População Rural/estatística & dados numéricos , Senegal/epidemiologia , Vigilância de Evento Sentinela , Estados Unidos , Organização Mundial da Saúde , Adulto JovemRESUMO
We tested for enterovirus D68 in fecal samples collected during June-September 2016 from 567 patients with acute flaccid paralysis in 7 West Africa nations. Children <5 years old comprised 64.3% of enterovirus D68 positive patients. Our findings emphasize the need for active surveillance for acute flaccid myelitis.
Assuntos
Enterovirus Humano D , Infecções por Enterovirus , Enterovirus , Mielite , África Ocidental , Viroses do Sistema Nervoso Central , Criança , Pré-Escolar , Enterovirus Humano D/genética , Infecções por Enterovirus/epidemiologia , Humanos , Doenças Neuromusculares , Paralisia/epidemiologiaRESUMO
The spread of severe acute respiratory syndrome coronavirus 2 began later in Africa than in Asia and Europe. Senegal confirmed its first case of coronavirus disease on March 2, 2020. By March 4, a total of 4 cases had been confirmed, all in patients who traveled from Europe.
Assuntos
Betacoronavirus , Infecções por Coronavirus/epidemiologia , Surtos de Doenças/estatística & dados numéricos , Transmissão de Doença Infecciosa/estatística & dados numéricos , Pneumonia Viral/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19 , Criança , Pré-Escolar , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Pandemias , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , SARS-CoV-2 , Senegal/epidemiologia , Adulto JovemRESUMO
To retrospectively investigate enterovirus D68 circulation in Senegal during the 2014 US outbreak, we retrieved specimens from 708 persons, mostly children, who had acute respiratory symptoms during September-December 2014. Enterovirus D68 was detected in 14 children (2.1%); most cases occurred in October. Phylogenetic analysis revealed that all strains clustered within subclade A1.
Assuntos
Surtos de Doenças , Enterovirus Humano D/classificação , Enterovirus Humano D/genética , Infecções por Enterovirus/epidemiologia , Infecções por Enterovirus/virologia , Carga Viral , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , DNA Viral , Infecções por Enterovirus/história , Feminino , Genótipo , História do Século XXI , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Filogenia , Estudos Retrospectivos , Estações do Ano , Senegal/epidemiologia , Análise de Sequência de DNA , Adulto JovemAssuntos
Febre de Chikungunya , Vírus Chikungunya , Genótipo , Técnicas de Diagnóstico Molecular , Humanos , Febre de Chikungunya/diagnóstico , Febre de Chikungunya/sangue , Febre de Chikungunya/virologia , Técnicas de Diagnóstico Molecular/métodos , Vírus Chikungunya/genética , Vírus Chikungunya/isolamento & purificação , África Ocidental , Sensibilidade e Especificidade , Estados Unidos , Centers for Disease Control and Prevention, U.S.RESUMO
BACKGROUND: Human metapneumovirus (HMPV) is a causal agent of acute respiratory infection, especially in primarily children. At the clinical level, HMPV is associated to several diseases including bronchitis, croup, pneumonia, bronchiolitis, reactive airway disease, chronic obstructive pulmonary disease and asthma exacerbations, specifically in children less than 5 years. Here, we carried out a retrospective pilot study, based on the processing of nasopharyngeal swabs, with a focus on the epidemiology and molecular characteristics of HMPV in Senegal. METHODS: This retrospective study was conducted from January 2012 to December 2016. Briefly, all outpatients presenting to healthcare sentinel sites were screened for surveillance enrollment and included if they met criteria for ILI. Naso-oropharyngeal swabs were collected from eligible participants. For viral respiratory pathogens detection, including HMPV, the Anyplex™ II RV16 Detection kit was used. A fragment of the hMPV F gene was targeted for sequencing. RESULTS: In total, 8209 patients with ILI were enrolled. Half of them (49.7%) were children under 5 years. Fever was the most common symptom followed by cough, and rhinitis. Three hundred eight patients were positive for HMPV (3.75%). 89 (28.9%) were detected as single infection. In co-infection cases, the most common co-infecting viruses were influenza, adenovirus and rhinovirus. HMPV detection rates in the different age groups varied significantly with the children under 5 years group accounting for 71.7% of positive patients. The temporal distribution pattern for HMPV infection showed a clear seasonal pattern with a higher activity during the rainy period (July-September). Phylogenetic analyses revealed that HMPV specimens circulating in Senegal were distributed into the two main genetic lineages, A and B. We also noted a co-circulation of both genetic lineages during the whole study period except in 2014. CONCLUSION: In summary, the present study characterized the recent prevalence, seasonality and genetic diversity of HMPV in a large outpatient population presented with ILI in Senegal between 2012 and 2016. Globally our results show a clear seasonal circulation pattern of HMPV in Senegal. Our findings identified children less than 5 years as more susceptible group to HMPV infection. Molecular studies identified A2, B1 and B2 as the major genotypes circulating.
Assuntos
Metapneumovirus/genética , Infecções por Paramyxoviridae/epidemiologia , Infecções Respiratórias/virologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Coinfecção/virologia , Feminino , Genótipo , Humanos , Lactente , Influenza Humana/etiologia , Masculino , Metapneumovirus/patogenicidade , Pessoa de Meia-Idade , Pacientes Ambulatoriais/estatística & dados numéricos , Infecções por Paramyxoviridae/etiologia , Filogenia , Projetos Piloto , Prevalência , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/etiologia , Estudos Retrospectivos , Senegal/epidemiologiaRESUMO
BACKGROUND: Acute Respiratory Infections (ARI) are common causes of febrile illnesses in many settings in Senegal. These infections are usually managed presumptively due to lack of appropriate diagnostic tools. This situation, can lead to poor management of febrile illness or antibiotic misuse. In addition, there are limited data on the spectrum of pathogens commonly responsible for these ARI. This study was conducted to explore the pathogens community among patients with acute respiratory infection in a rural area in Senegal. METHODS: A cross sectional study was conducted from August to December 2015. Children and adult patients attending Keur Socé health post for signs suggestive of acute respiratory infection were enrolled after providing inform consent. Eligible participants were recruited using a consecutive sampling method. Paired nose and throat swabs were collected for pathogen detection. Samples were processed using a multiplex PCR designed to identify 21 pathogens including both virus and bacteria. RESULTS: Two hundred and fifty patients participated in the study. Samples positivity rate was evaluated at 95.2% (238/250). Streptococcus pneumoniae was the predominant pathogen (74%) and was present in all months and all age-groups, followed by Staphylococcus aureus (28,8%) and rhinovirus (28,4%). Respiratory syncytial virus (RSV) was detected only among children under 5 years old in August and September while coronavirus was present in all age groups, during the months of October and December. CONCLUSION: This pilot study revealed a diversity of pathogens over the time and across all age groups, highlighting the need for further exploration. A pathogen community approach including both virus and bacteria at a larger scale becomes crucial for a better understanding of transmission dynamics at population level in order to help shape ARI control strategies.
Assuntos
Malária/complicações , Vírus Sincicial Respiratório Humano/isolamento & purificação , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Rhinovirus/isolamento & purificação , Staphylococcus aureus/isolamento & purificação , Streptococcus pneumoniae/isolamento & purificação , Adolescente , Criança , Pré-Escolar , Estudos Transversais , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Feminino , Humanos , Lactente , Malária/diagnóstico , Malária/transmissão , Masculino , Reação em Cadeia da Polimerase Multiplex , RNA Viral/genética , RNA Viral/metabolismo , Vírus Sincicial Respiratório Humano/genética , Infecções Respiratórias/complicações , Infecções Respiratórias/diagnóstico , Rhinovirus/genética , População Rural , Estações do Ano , Senegal , Staphylococcus aureus/genética , Streptococcus pneumoniae/genéticaRESUMO
BACKGROUND: The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion. RESULTS: Here we report the first complete assembly of E. cuniculi chromosome ends, and describe a novel mosaic structure of segmental duplications (EXT repeats) in these regions. EXT repeats range in size between 3.5 and 23.8 kbp and contain four multigene families encoding membrane associated proteins. Twenty-one recombination sites were identified in the sub-terminal region of E. cuniculi chromosomes. Our analysis suggests that these sites contribute to the diversity of chromosome ends organization through Double Strand Break repair mechanisms. The region containing EXT repeats at chromosome extremities can be differentiated based on gene composition, GC content, recombination sites density and chromosome landscape. CONCLUSION: Together this study provides the complete structure of the chromosome ends of E. cuniculi GB-M1, and identifies important factors, which could play a major role in parasite diversity and host-parasite interactions. Comparison with other eukaryotic genomes suggests that terminal regions could be distinguished precisely based on gene content, genetic instability and base composition biais. The diversity of processes assciated with chromosome extremities and their biological consequences, as they are presented in the present study, emphasize the fact that great effort will be necessary in the future to characterize more carefully these regions during whole genome sequencing efforts.
Assuntos
Encephalitozoon cuniculi/genética , Interações Hospedeiro-Parasita/genética , Sequências Repetitivas de Ácido Nucleico/genética , Telômero/genética , Composição de Bases , DNA de Protozoário/genética , Genoma , Família Multigênica/genéticaRESUMO
BACKGROUND: In Africa, especially in West Africa, studies about the prevalence and diversity of respiratory viruses (influenza and others) in elderly people are largely lacking. In studies done elsewhere, it is well established that older people, when compared with younger adults, are at greater risk of significant morbidity and mortality from complications arising from influenza. The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. METHODS: The recruitment period of this study was from January 2009 to December 2011. 232 patients aged 50 years and above presenting ILI cases were enrolled. Nasal-pharyngeal and/or oral pharyngeal swabs were collected from patients. RNA was extracted from 200 µl of each sample followed by a two-step real-time RT-PCR. The Anyplex™ II RV16 Detection kit was used for viral detection. The kit enabled the simultaneous detection of the presence of 16 respiratory viruses. RESULTS: 150 viruses were detected: influenza viruses (44.7%) and rhinoviruses (26.7%) were the most prevalent. We detected 13 human parainfluenza viruses (8.7%), 7 human respiratory syncytial viruses (4.7%), 6 coronaviruses (4%), 5 human metapneumoviruses (3.3%), 5 human adenoviruses (3.3%) and 1 human bocavirus (0.7%). 14 cases (6%) of dual virus infections and one triple viral detection case were encountered. 56 (56.6%) viruses detected were found in the 50-64 year old age group, 59 (76.6%; P < 0.001) from 65-74 year old age group and 35 (62.5%) were detected in the ≥75 year old age group. The viral co-infections were more frequent in the 65-74 age group (9/15). CONCLUSIONS: This pilot study demonstrates a variety of respiratory viruses in the elderly. It also highlights a high prevalence of these viruses in this age group. We speculate from these results that the impact of respiratory viruses other than influenza on the elderly has been considerably underestimated. A more exhaustive study seems necessary in order to provide a more complete picture of the burden of respiratory viruses on morbidity among adults over 50 years old in the sub-Saharan context.
Assuntos
Infecções Respiratórias/epidemiologia , Viroses/epidemiologia , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Coinfecção/diagnóstico , Coinfecção/epidemiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Projetos Piloto , Prevalência , Estudos Prospectivos , Reação em Cadeia da Polimerase em Tempo Real , Infecções Respiratórias/diagnóstico , Senegal/epidemiologia , Viroses/diagnósticoRESUMO
Acute respiratory viruses (ARVs) are the leading cause of diseases in humans worldwide. High-risk individuals, including children and the elderly, could potentially develop severe illnesses that could result in hospitalization or death in the worst case. The most common ARVs are the Human respiratory syncytial virus, Human Metapneumovirus, Human Parainfluenza Virus, rhinovirus, coronaviruses (including SARS and MERS CoV), adenoviruses, Human Bocavirus, enterovirus (-D68 and 71), and influenza viruses. The olfactory deficits due to ARV infection are a common symptom among patients. This review provides an overview of the role of SARS-CoV-2 and other common ARVs in the development of human olfactory pathophysiology. We highlight the critical need to understand the signaling underlying the olfactory dysfunction and the development of therapeutics for this wide-ranging category of AVRs to restore the altered or loss of smell in affected patients.
RESUMO
OBJECTIVES: Several factors can cause acute flaccid paralysis cases including non-polio enteroviruses. In Senegal, few studies on non-polio enteroviruses (NPEV) have been performed. METHODS: Our study assess the molecular epidemiology of non-polio enteroviruses in Senegal from 2013 to 2021 through the previously existing programs for surveillance of polioviruses. RESULTS: A total of 3815 stool samples and 281 sewage samples were collected. After virus isolation by cell culture, non-polio enteroviruses-positive isolates were confirmed by reverse transcriptase-quantitative polymerase chain reaction. Following this detection, the positive samples were subjected to molecular characterization. Our data showed that 15.22% and 52.66% were positive in cell culture for non-polio enteroviruses in acute flaccid paralysis surveillance and environmental surveillance, respectively. These non-polio enteroviruses-positive isolates were detected all year round but tend to unequal peaks of circulation, and the age group 0-5 years was more vulnerable to infection (84.4%). Genetic characterization revealed the circulation of enteroviruses species infecting humans (Enterovirus A - Enterovirus D): Enterovirus A (29.2%) and Enterovirus B (63.1%) isolates from both the acute flaccid paralysis surveillance and environmental surveillance while Enterovirus C (5.3%) and Enterovirus D (2.4%) were only isolated from the acute flaccid paralysis surveillance. However, the highly prevalent Enterovirus B species from the acute flaccid paralysis surveillance included echovirus 7 and echovirus 13, whereas coxsackievirus A6 was the predominant species from the environmental surveillance. CONCLUSION: This first 8-year period study of NPEV in Senegal showed that NPEV represent important viral etiologies associated with acute flaccid paralysis cases and circulating in environmental surveillance in Senegal and highlighted the need to promote effective long-term strategies for monitoring of non-polio enteroviruses infections.
Assuntos
Infecções por Enterovirus , Enterovirus , Humanos , Recém-Nascido , Lactente , Pré-Escolar , Esgotos , Senegal/epidemiologia , Paralisia/epidemiologia , Enterovirus/genética , Infecções por Enterovirus/epidemiologia , Enterovirus Humano B , Antígenos ViraisRESUMO
In Senegal, since its first detection in early March 2020, genomic surveillance of SARS-CoV-2 isolates has led to the identification of the emergence of the Omicron BA.4 and BA.5 sublineages from early June 2022. To investigate the origin of a cluster of cases in Northern Senegal on July 2022, isolates were analysed using Next-generation sequencing and phylogeny. Our data provided evidence of the origin of the cluster of BA.4 cases from a XAS recombinant, that is to date, the first reported sequence of this variant from Senegal. Continuous genomic surveillance of positive SARS-CoV-2 samples is a crucial need.
Assuntos
Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Senegal , Filogenia , SARS-CoV-2/genéticaRESUMO
Two bacteriophages (phages) of Klebsiella pneumoniae were isolated from sewage water collected from Dakar, Senegal. Phage vKpIN17 belongs to the Przondovirus genus within the Autographiviridae family, with double-stranded DNA genomes, whereas vKpIN18 belongs to the Webervirus genus of the Drexlerviridae family.
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Background: With growing use of parasitological tests to detect malaria and decreasing incidence of the disease in Africa; it becomes necessary to increase the understanding of causes of non-malaria acute febrile illness (NMAFI) towards providing appropriate case management. This research investigates causes of NMAFI in pediatric out-patients in rural Guinea-Bissau. Methods: Children 0-5 years presenting acute fever (≥38°) or history of fever, negative malaria rapid diagnostic test (mRDT) and no signs of specific disease were recruited at the out-patient clinic of 3 health facilities in Bafatá province during 54 consecutive weeks (dry and rainy season). Medical history was recorded and blood, nasopharyngeal, stool and urine samples were collected and tested for the presence of 38 different potential aetiological causes of fever. Results: Samples from 741 children were analysed, the protocol was successful in determining a probable aetiological cause of acute fever in 544 (73.61%) cases. Respiratory viruses were the most frequently identified pathogens, present in the nasopharynx samples of 435 (58.86%) cases, followed by bacteria detected in 167 (22.60%) samples. Despite presenting negative mRDTs, P. falciparum was identified in samples of 24 (3.25%) patients. Conclusions: This research provides a description of the aetiological causes of NMAFI in West African context. Evidence of viral infections were more commonly found than bacteria or parasites.