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1.
Int J Infect Dis ; 84: 99-101, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31096054

RESUMO

In January 2019, an outbreak of chikungunya virus fever was reported in a rural region near Pointe-Noire, Republic of the Congo. Molecular and phylogenetic analysis of this new CHIKV strain demonstrated the presence of the A226V substitution and a surprisingly close relation with Aedes aegypti-associated Central Africa chikungunya strains. These results, combined with the preponderance of Aedes albopictus in the outbreak area, suggest a recent vector-host switch facilitated by the emergence and spread of the A226V mutation from a related CHIKV strain previously circulating in Aedes aegypti. The proximity of this outbreak to the large city of Pointe-Noire alerts us to a possibly devastating future outbreak in the absence of measures limiting the proliferation of Ae. albopictus mosquitoes.


Assuntos
Febre de Chikungunya/epidemiologia , Aedes/virologia , Animais , Febre de Chikungunya/transmissão , Vírus Chikungunya/genética , Congo/epidemiologia , Surtos de Doenças , Humanos , Mosquitos Vetores/classificação , Mosquitos Vetores/genética , Mutação , Filogenia , Fatores de Tempo
3.
J Gen Virol ; 100(6): 911-912, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31021739

RESUMO

Members of the family Filoviridae produce variously shaped, often filamentous, enveloped virions containing linear non-segmented, negative-sense RNA genomes of 15-19 kb. Several filoviruses (e.g., Ebola virus) are pathogenic for humans and are highly virulent. Several filoviruses infect bats (e.g., Marburg virus), whereas the hosts of most other filoviruses are unknown. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on Filoviridae, which is available at www.ictv.global/report/filoviridae.

4.
Sci Rep ; 9(1): 1504, 2019 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-30728408

RESUMO

Human papillomavirus (HPV) is recognised as the cause of precancerous and cancerous cervical lesions. Furthermore, in high-grade lesions, HPV is frequently integrated in the host cell genome and associated with the partial or complete loss of the E1 and E2 genes, which regulate the activity of viral oncoproteins E6 and E7. In this study, using a double-capture system followed by high-throughput sequencing, we determined the HPV integration status present in liquid-based cervical smears in an urban Gabonese population. The main inclusion criteria were based on cytological grade and the detection of the HPV16 genotype using molecular assays. The rate of HPV integration in the host genome varied with cytological grade: 85.7% (6/7), 71.4% (5/7), 66.7% (2/3) 60% (3/5) and 30.8% (4/13) for carcinomas, HSIL, ASCH, LSIL and ASCUS, respectively. For high cytological grades (carcinomas and HSIL), genotypes HPV16 and 18 represented 92.9% of the samples (13/14). The integrated form of HPV16 genotype was mainly found in high-grade lesions in 71.4% of samples regardless of cytological grade. Minority genotypes (HPV33, 51, 58 and 59) were found in LSIL samples, except HPV59, which was identified in one HSIL sample. Among all the HPV genotypes identified after double capture, 10 genotypes (HPV30, 35, 39, 44, 45, 53, 56, 59, 74 and 82) were detected only in episomal form. Our study revealed that the degree of HPV integration varies with cervical cytological grade. The integration event might be a potential clinical prognostic biomarker for the prediction of the progression of neoplastic lesions.

5.
Arch Virol ; 164(4): 1233-1244, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30663023

RESUMO

In October 2018, the order Mononegavirales was amended by the establishment of three new families and three new genera, abolishment of two genera, and creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).


Assuntos
Mononegavirais/classificação , Mononegavirais/genética , Mononegavirais/isolamento & purificação , Filogenia , Virologia/organização & administração
6.
Infect Genet Evol ; 68: 43-46, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30529088

RESUMO

Astroviruses (AstVs) are mostly responsible for mild to severe gastroenteritis infections in humans and animals. AstVs infect a wide range of host species, have a large genetic diversity with different circulating variants and are thus a high zoonotic risk for human populations. Among these host species, rodents are known to harbor several AstVs variants. Therefore, it is important to identify in rodent species which AstVs are circulating and evaluate their potential zoonotic risk for humans. In this context, this study aimed to screen the presence of AstVs in 267 rodents trapped in 2012 in Franceville and Makokou, two cities in Gabon. RNA extracted from grinded intestines were used for the screening of AstVs by amplification of a conserved region of the RNA dependent RNA polymerase. Results report the identification of AstVs in 12 individuals (4.6% rate), belonging to three different species including Rattus rattus, Mus musculus and Hybomys univittatus. These findings report the first identification of AstVs in R. rattus and H. univittatus. The phylogenetic analyses indicate host specificity of rodents AstVs. The absence of rodent AstVs within the human AstV clade suggests a low rate of interspecies transmission of these viruses and consequently a low zoonotic risk.

7.
J Viral Hepat ; 2018 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-30141209

RESUMO

Although central Africa is classified as having a high endemicity of hepatitis B virus (HBV) and hepatitis D virus (HDV) infection, there is paucity of prevalence studies. For the first time on a country-wide level in Central Africa, we show in Gabon an overall 7.4% prevalence of Hepatitis B surface antigen (HBsAg) and that more than 25% of the HBsAg-positive population are infected by HDV. Although HBV prevalence did not differ significantly between provinces, there is a north-south split in the distribution of HDV seroprevalence, with the highest rates (>66.0%) correlating with the presence of specific ethnic groups in the northeastern provinces. Genotyping revealed high genetic diversity of the HBV and HDV strains circulating in Gabon, including many restricted to this region of the globe. This work confirmed that high exposure to HBV and HDV infection reported in selected regions of Gabon holds true across the whole country.

8.
BMC Res Notes ; 11(1): 495, 2018 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-30029615

RESUMO

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.


Assuntos
Diarreia/virologia , Bocavirus Humano/isolamento & purificação , Influenza Humana/virologia , Pré-Escolar , Feminino , Gabão , Humanos , Lactente , Vírus da Influenza A Subtipo H1N1 , Masculino , Infecções por Parvoviridae , Prevalência , Infecções Respiratórias , Estudos Retrospectivos
10.
Arch Virol ; 163(8): 2283-2294, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29637429

RESUMO

In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.


Assuntos
Mononegavirais/classificação , Animais , Humanos , Mononegavirais/genética , Mononegavirais/isolamento & purificação , Infecções por Mononegavirales/veterinária , Infecções por Mononegavirales/virologia , Filogenia
11.
Virus Res ; 247: 21-25, 2018 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-29421305

RESUMO

Canine distemper (CD) is the most deadly disease in dogs with mortality rates reaching 50%. The pathological agent, the CD virus (CDV), generally causes a severe systemic disease, although the nervous form can coexist with the acute catarrhal form in the same individual. In this study, we describe an outbreak of 18 cases of CD that occurred in 2015 in a German Shepherd dog population in northwestern Gabon. In addition, we determined the sequence of the CDV genotype associated with this fatal distemper infection in Gabon and compared it with other published CDV sequences. The CDV was detected using RT-PCR on cDNA from RNA of harvested brains and other organs. The identification was confirmed by sequencing amplicons. Moreover, we obtained the whole genome sequence using high-throughput sequencing. Phylogenetic analysis revealed that Gabonese CDV strain clustered with European strains belonging to the Europe genotype. This study provided the first molecular detection of the CDV strain associated with this fatal distemper infection in Central Africa region.


Assuntos
Vírus da Cinomose Canina/genética , Cinomose/epidemiologia , Genoma Viral , Filogenia , RNA Viral/genética , Animais , Encéfalo/patologia , Encéfalo/virologia , DNA Complementar/genética , Cinomose/mortalidade , Cinomose/transmissão , Cinomose/virologia , Vírus da Cinomose Canina/isolamento & purificação , Cães , Europa (Continente)/epidemiologia , Gabão/epidemiologia , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA , Análise de Sobrevida , Sequenciamento Completo do Genoma
12.
Intervirology ; 61(4): 174-184, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30625488

RESUMO

Non-malarial febrile illness outbreaks were documented in 2007 and 2010 in Gabon. After investigation, these outbreaks were attributed to the chikungunya and dengue viruses (CHIKV and DENV). However, for more than half of the samples analyzed, the causative agent was not identified. Given the geographical and ecological position of Gabon, where there is a great animal and microbial diversity, the circulation of other emerging viruses was suspected in these samples lacking aetiology. A total of 436 undiagnosed samples, collected between 2007 and 2013, and originating from 14 urban, suburban, and rural Gabonese locations were selected. These samples were used for viral isolation on newborn mice and VERO cells. In samples with signs of viral replication, cell supernatants and brain suspensions were used to extract nucleic acids and perform real-time RT-PCR targeting specific arboviruses, i.e., CHIKV, DENV, yellow fever, Rift Valley fever, and West Nile and Zika viruses. Virus isolation was conclusive for 43 samples either on newborn mice or by cell culture. Virus identification by RT-PCR led to the identification of CHIKV in 37 isolates. A total of 18 complete genomes and 19 partial sequences containing the E2 and E1 genes of CHIKV were sequenced using next-generation sequencing technology or the Sanger method. Phylogenetic analysis of the complete genomes showed that all the sequences belong to the East Central South Africa lineage. Furthermore, we identified 2 distinct clusters. The first cluster was made up of sequences from the western part of Gabon, whereas the second cluster was made up of sequences from the southern regions, reflecting the way CHIKV spread across the country following its initial introduction in 2007. Similar results were obtained when analyzing the CHIKV genes of the E2 and E1 structural proteins. Moreover, study of the mutations found in the E2 and E1 structural proteins revealed the presence of several mutations that facilitate the adaptation to the Aedes albopictus mosquito, such as E2 I211T and E1 A226V, in all the Gabonese CHIKV strains. Finally, sequencing of 6 additional viral isolates failed to lead to any conclusive identification.


Assuntos
Febre de Chikungunya/epidemiologia , Surtos de Doenças , Febre de Causa Desconhecida/diagnóstico , Vírus/isolamento & purificação , Animais , Animais Recém-Nascidos , Cercopithecus aethiops , Gabão/epidemiologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Camundongos , Filogenia , Reação em Cadeia da Polimerase em Tempo Real , Células Vero , Vírus/classificação , Vírus/genética
13.
Virol J ; 14(1): 241, 2017 12 21.
Artigo em Inglês | MEDLINE | ID: mdl-29268766

RESUMO

BACKGROUND: Cervical cancer is the fourth most common malignancy in women worldwide. However, screening with human papillomavirus (HPV) molecular tests holds promise for reducing cervical cancer incidence and mortality in low- and middle-income countries. The performance of the Abbott RealTime High-Risk HPV test (AbRT) was evaluated in 83 cervical smear specimens and compared with a conventional nested PCR coupled to high-throughput sequencing (HTS) to identify the amplicons. RESULTS: The AbRT assay detected at least one HPV genotype in 44.57% of women regardless of the grade of cervical abnormalities. Except for one case, good concordance was observed for the genotypes detected with the AbRT assay in the high-risk HPV category determined with HTS of the amplicon generated by conventional nested PCR. CONCLUSIONS: The AbRT test is an easy and reliable molecular tool and was as sensitive as conventional nested PCR in cervical smear specimens for detection HPVs associated with high-grade lesions. Moreover, sequencing amplicons using an HTS approach effectively identified the genotype of the hrHPV identified with the AbRT test.


Assuntos
Técnicas de Diagnóstico Molecular/métodos , Técnicas de Diagnóstico Molecular/normas , Papillomaviridae/genética , Infecções por Papillomavirus/virologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Colo do Útero/virologia , DNA Viral/análise , Feminino , Gabão , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Papillomavirus Humano 16/genética , Papillomavirus Humano 18/genética , Humanos , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase Multiplex , Papillomaviridae/classificação , Papillomaviridae/isolamento & purificação , Infecções por Papillomavirus/diagnóstico , Reação em Cadeia da Polimerase , Sensibilidade e Especificidade , Neoplasias do Colo do Útero/virologia , Esfregaço Vaginal
14.
PLoS One ; 12(10): e0185569, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28968427

RESUMO

Few studies have analyzed the gut microbiota of child in unindustrialized countries, but none during the first month of life. Stool samples were collected from healthy newborns in hospitals of Gabon (n = 6) and Republic of the Congo (n = 9) at different time points during the first month of life: meconium, day 2 (D02), day 7 (D07) and day 28 (D28). In addition, one fecal sample was collected from each mother after delivery. Metagenomic sequencing was performed to determine the bacterial communities, and multiplex real-time PCR was used to detect the presence of seven enteric viruses (rotavirus a, adenovirus, norovirus I and II, sapovirus, astrovirus, enterovirus) in these samples. Bacterial diversity was high in the first days of life, and was dominated by the genus Prevotella. Then, it rapidly decreased and remained low up to D28 when the gut flora was composed almost exclusively of strictly anaerobic bacteria. Each infant's fecal bacterial microbiota composition was significantly closer to that of their mother than to that of any other woman in the mothers' group, suggesting an intrauterine, placental or amniotic fluid origin of such bacteria. Moreover, bacterial communities differed according to the delivery mode. Overall, the bacterial microbiota communities displayed a similar diversification and expansion in newborns within and between countries during the first four weeks of life. Moreover, six of the fifteen infants of this study harbored enteric viruses (rotavirus, enterovirus and adenovirus) in fecal samples, but never in the meconium. A maternal source for the viruses detected at D02 and D07 can be excluded because none of them was found also in the child's mother. These findings improve our knowledge on the gut bacterial and viral communities of infants from two Sub-Saharan countries during their first month of life.


Assuntos
Fezes/microbiologia , Fezes/virologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Parto Obstétrico/métodos , República Democrática do Congo , Enterovirus/classificação , Enterovirus/genética , Enterovirus/isolamento & purificação , Feminino , Gabão , Humanos , Recém-Nascido , Masculino , Metagenoma , Reação em Cadeia da Polimerase em Tempo Real
16.
J Parasitol ; 103(4): 330-337, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28509658

RESUMO

Haemosporidian parasites are protozoans that infect many different vertebrate hosts. Re-examination of the diversity of haemosporidian parasites, using molecular tools, has generally led to rearrangements of traditional classifications. In this study, we explored the diversity of haemosporidian parasites infecting some species of reptile and birds living in the forests of Gabon, Central Africa, by analyzing a collection of 128 samples of reptiles and birds. We found that samples from 2 tortoise species (Pelusios castaneus and Kinixys erosa) and 3 bird species (Turtur afer, Ceratogymna atrata, and Agelastes niger) were infected by Haemocystidium spp. and Parahaemoproteus spp., respectively. From an ecological point of view, these lineages of parasites do not show host specificity because we have found them in several host species (2 tortoise and 3 bird species) that come from different areas of Gabon forest which are infected with these parasites. Also, our phylogenetic analyses revealed that the obtained lineages are related to isolates from other continents found in the same groups of vertebrates. Thus, our results show that haemosporidian parasites are also infecting central African vertebrates and that new lineages of these parasites are circulating in wild animals of the Gabon forest.


Assuntos
Doenças das Aves/parasitologia , Columbidae/parasitologia , Galliformes/parasitologia , Haemosporida/classificação , Infecções Protozoárias em Animais/parasitologia , Tartarugas/parasitologia , Animais , Animais Selvagens , Aves , Citocromos b/genética , DNA de Protozoário/sangue , DNA de Protozoário/isolamento & purificação , Florestas , Gabão , Variação Genética , Haemosporida/genética , Fígado/parasitologia , Filogenia , Baço/parasitologia
17.
Viruses ; 9(5)2017 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-28492506

RESUMO

The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel "filovirus." Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.


Assuntos
Filoviridae/classificação , Filoviridae/genética , Filogenia , Algoritmos , Sequência de Bases , Bases de Dados de Ácidos Nucleicos , Ebolavirus/classificação , Ebolavirus/genética , Variação Genética , Genoma Viral , Marburgvirus/classificação , Marburgvirus/genética , Mononegavirais/classificação , Mononegavirais/genética , Análise de Sequência de DNA , Desenho de Programas de Computador , Especificidade da Espécie , Sequenciamento Completo do Genoma
18.
Arch Virol ; 162(8): 2493-2504, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28389807

RESUMO

In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).


Assuntos
Genoma Viral , Mononegavirais/classificação , Ordem dos Genes , Mononegavirais/genética , Filogenia , Especificidade da Espécie
19.
Syst Biol ; 66(3): 463-473, 2017 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-27798405

RESUMO

Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment. [Arenaviridae; binomials; ICTV; International Committee on Taxonomy of Viruses; Mononegavirales; virus nomenclature; virus taxonomy.].


Assuntos
Classificação , Vírus , Terminologia como Assunto
20.
Infect Agent Cancer ; 11(1): 50, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27610192

RESUMO

BACKGROUND: The human papillomavirus (HPV) is the causative agent of cervical cancer, which is the leading cancer-related cause of death for women in Sub-Saharan Africa. In 2013, the Gabonese Ministry of Health and the Sylvia Bongo Ondimba Foundation implemented cervical cancer screening programs based on the detection of cancerous lesions by visual inspection with acetic acid and/or Lugol's iodine (VIA/VILI). This pilot study was set up to determine the HPV profile and analyze the nucleotide sequence variation of HPV16 circulating in patients with cervical abnormalities detected by VIA/VILI testing. METHODS: The cervical abnormalities observed upon VIA/VILI were confirmed by liquid-based cytology for all tested women. Nested PCR using the MY09/11 and GP5+/6+ primer sets was used to detect HPVs present in the extracted DNA. HPV genotypes were determined after sequencing of amplicons based on a high-throughput sequencing approach. For isolates of the HPV16 genotype, the E6 gene and the long control region (LCR) were directly sequenced using Sanger method. RESULTS: The study included 87 women who showed a positive VIA/VILI result. Cervical abnormalities were found in 40.23 % of women and 40 % were classified as high-grade lesions. The HPV detection rate was 82.9 % among women with abnormal cytology. Among all the identified high-risk HPV genotypes, HPV16, 18 and 33 were the most frequent. Multiple HPV infections were observed in 42.31 % of HPV-infected women. Analysis of the HPV16 sequence variation in the E6 gene and in the LCR showed that 85.3 and 14.7 % belonged to the African and European lineages, respectively. Among the African branch variants, Af2 was the most frequently identified in this study. CONCLUSION: This study offers the first report of the HPV detection rate and molecular epidemiology among Gabonese women with a positive result in a VIA/VILI screening test. Moreover, data on the HPV16 sequence variation confirm the predominance of African variants in high-grade lesions.

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