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1.
medRxiv ; 2021 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-34031660

RESUMO

COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences. In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.

2.
Virol J ; 17(1): 114, 2020 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-32709248

RESUMO

BACKGROUND: Detection of HIV-1 transmitted drug resistance (TDR) and subtype diversity (SD) are public health strategies to assess current HIV-1 regimen and ensure effective therapeutic outcomes of antiretroviral therapy (ART) among HIV-1 patients. Globally, limited data exist on TDR and SD among blood donors. In this study, drug resistance mutations (DRMs) and SD amongst HIV-1 sero-positive blood donors in Accra, Ghana were characterized. METHODS: Purposive sampling method was used to collect 81 HIV sero-positive blood samples from the Southern Area Blood Center and confirmed by INNO-LIA as HIV-1 and/or HIV-2. Viral RNA was only extracted from plasma samples confirmed as HIV-1 positive. Complementary DNA (cDNA) was synthesized using the RNA as a template and subsequently amplified by nested PCR with specific primers. The expected products were verified, purified and sequenced. Neighbour-joining tree with the Kimura's 2-parameter distances was generated with the RT sequences using Molecular Evolutionary Genetic Analysis version 6.0 (MEGA 6.0). RESULTS: Out of the 81 plasma samples, 60 (74%) were confirmed as HIV-1 sero-positive by INNO-LIA HIVI/II Score kit with no HIV-2 and dual HIV-1/2 infections. The remaining samples, 21 (26%) were confirmed as HIV sero-negative. Of the 60 confirmed positive samples, (32) 53% and (28) 47% were successfully amplified in the RT and PR genes respectively. Nucleotide sequencing of amplified samples revealed the presence of major drug resistance mutations in two (2) samples; E138A in one sample and another with K65R. HIV-1 Subtypes including subtypes A, B, CRF02_AG and CRF09_cpx were found. CONCLUSION: This study found major drug resistance mutations, E138A and K65R in the RT gene that confer high level resistance to most NNRTIs and NRTI respectively. CRF02_AG was most predominant, the recorded percentage of subtype B and the evolutionary relationship inferred by phylogenetic analysis may suggest possible subtype importation. However, a more prospective and detailed analysis is needed to establish this phenomenon. The data obtained would inform the selection of drugs for ART initiation to maximize therapeutic options in drug-naïve HIV-1 patients in Ghana.


Assuntos
Doadores de Sangue , Farmacorresistência Viral/genética , HIV-1/genética , Mutação , Filogenia , Adulto , Fármacos Anti-HIV/farmacologia , Doadores de Sangue/estatística & dados numéricos , Estudos Transversais , Feminino , Gana , Infecções por HIV/virologia , HIV-1/classificação , HIV-1/efeitos dos fármacos , Humanos , Masculino , Pessoa de Meia-Idade , RNA Viral/genética , Adulto Jovem
3.
BMC Infect Dis ; 19(1): 533, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208352

RESUMO

BACKGROUND: Distribution of Hepatitis C virus (HCV) genotypes varies significantly worldwide. Genomic diversity between genotypes has implications for treatment, vaccine development and optimal design of HCV diagnostic assays. Molecular characterization of HCV in different geographical areas is therefore very essential for management and public health control of HCV infection. This study investigated the molecular epidemiology and characteristics of HCV genotypes in healthy individuals in Accra, Ghana. METHODS: An experimental study was carried out on blood samples obtained from voluntary blood donors. Two hundred samples were initially screened for HCV antibodies and infection was confirmed by RNA detection through RT-PCR of the 5'-untranslated region (5'UTR). The core gene sequences were analysed for HCV genotype determination by genotype-specific PCR; and then by cloning and direct sequencing followed by phylogenetic analysis. The sequences were further analysed in detail by similarity plotting. RESULTS: Molecular diagnosis confirmed the presence of HCV RNA in 2 out of 200 (1%) blood donors. Initial genotyping by genotype-specific PCR identified all two infections as subtypes 2a and 2b of genotype 2. Extensive evolutionary and genetic analyses indicated two epidemiological profiles. First, phylogenetic tree topologies clearly showed that, collectively, the core sequences of the Ghanaian HCV isolates belong to a single, distinct genetic group within HCV genotype 2 cluster, with high genetic similarity and rapid sequence variation in a single individual. Second, the sequences are mosaics comprising 2e and other genotype 2 subtype fragments. The analyses underscore a unique and complex HCV genotype 2 core sequence profile of the Ghanaian isolates. CONCLUSIONS: Analysis of HCV core encoding sequences from Ghanaian blood donors in Accra confirmed predominance of genotype 2 HCV among healthy individuals. However, the isolates could not be classified into subtypes, possibly due to their complex sequence pattern that might suggest high mutability of the prevailing genotype. The core region of Ghanaian HCV therefore may not be suitable for distinguishing subtypes. These findings extend those from previous studies and thus underscore the need to search for subtype-informative region of Ghanaian HCV to elucidate the genetic diversity and factors determining outcome of HCV infections in Ghana.


Assuntos
Doadores de Sangue , Hepacivirus/genética , Hepatite C/virologia , Estudos Transversais , Genótipo , Gana/epidemiologia , Hepacivirus/isolamento & purificação , Hepatite C/epidemiologia , Anticorpos Anti-Hepatite C/sangue , Humanos , Epidemiologia Molecular , Filogenia , Reação em Cadeia da Polimerase
4.
J Med Microbiol ; 66(11): 1663-1672, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29068286

RESUMO

PURPOSE: There have been hardly any reports on the human immunodeficiency virus type 1 (HIV-1) drug-resistance profile from northern Ghana since antiretroviral therapy (ART) was introduced over a decade ago. This study investigated prevailing HIV-1 subtypes and examined the occurrence of drug resistance in ART-experienced patients in Tamale, the capital of the Northern Region of Ghana. METHODOLOGY: A cross-sectional study was carried out on HIV-infected adult patients receiving first-line ART. HIV viral load (VL) and CD4+ T-cell counts were measured. The pol gene sequences were analysed for genotypic resistance by an in-house HIV-1 drug-resistance test; the prevailing HIV-1 subtypes were analysed in detail.Results/Key findings. A total of 33 subjects were studied. Participants comprised 11 males (33.3 %) and 22 (66.7 %) females, with a median age of 34.5 years [interquartile range (IQR) 30.0-40.3]. The median duration on ART was 12 months (IQR 8.0-24). Of the 24 subjects successfully genotyped, 10 (41.7 %) viruses possessed at least one mutation conferring resistance to nucleoside or non-nucleoside reverse-transcriptase inhibitors (NRTIs/NNRTIs). Two-class drug resistance to NRTI and NNRTI was mostly detected (25 %, 6/24). The most frequent mutations were lamivudine-resistance M184V and efavirenz/nevirapine-resistance K103N. HIV-1 subtype CRF02_AG was predominant (79.2 %). Other HIV-1 subtypes detected were G (8.3 %), A3 (4.2 %) and importantly two (8.3 %) unique HIV-1 recombinant forms with CRF02_AG/A3 mosaic. CONCLUSION: HIV-1 shows high genetic diversity and on-going viral genetic recombination in the study region. Nearly 42 % of the patients studied harboured a drug-resistant virus. The study underscores the need for continued surveillance of HIV-1 subtype diversity; and of drug-resistance patterns to guide selection of second-line regimens in northern Ghana.


Assuntos
Fármacos Anti-HIV/farmacologia , Farmacorresistência Viral/genética , Infecções por HIV/epidemiologia , Infecções por HIV/virologia , HIV-1/genética , Adulto , Contagem de Linfócito CD4 , Estudos Transversais , Feminino , Genótipo , Gana/epidemiologia , Humanos , Masculino , Mutação , Filogenia , Prevalência , RNA Viral , Carga Viral
5.
Biomed Res Int ; 2017: 5245021, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28286767

RESUMO

Infectious diseases are a significant burden on public health and economic stability of societies all over the world. They have for centuries been among the leading causes of death and disability and presented growing challenges to health security and human progress. The threat posed by infectious diseases is further deepened by the continued emergence of new, unrecognized, and old infectious disease epidemics of global impact. Over the past three and half decades at least 30 new infectious agents affecting humans have emerged, most of which are zoonotic and their origins have been shown to correlate significantly with socioeconomic, environmental, and ecological factors. As these factors continue to increase, putting people in increased contact with the disease causing pathogens, there is concern that infectious diseases may continue to present a formidable challenge. Constant awareness and pursuance of effective strategies for controlling infectious diseases and disease emergence thus remain crucial. This review presents current updates on emerging and neglected infectious diseases and highlights the scope, dynamics, and advances in infectious disease management with particular focus on WHO top priority emerging infectious diseases (EIDs) and neglected tropical infectious diseases.


Assuntos
Doenças Transmissíveis Emergentes , Efeitos Psicossociais da Doença , Doenças Negligenciadas , Doenças Transmissíveis Emergentes/diagnóstico , Doenças Transmissíveis Emergentes/economia , Doenças Transmissíveis Emergentes/epidemiologia , Doenças Transmissíveis Emergentes/terapia , Humanos , Doenças Negligenciadas/diagnóstico , Doenças Negligenciadas/economia , Doenças Negligenciadas/epidemiologia , Doenças Negligenciadas/terapia
6.
BMC Womens Health ; 15: 46, 2015 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-26040938

RESUMO

BACKGROUND: Intravaginal practices may affect the colonization of vaginal flora and lead to vaginal infections due to the potential effects on the vaginal environment. This study investigated the vaginal practices and their possible effects on vaginal lactobacilli flora colonization in women in Accra. METHODS: A cross-sectional, descriptive single-site study was carried out on 141 women assessing medical care at the Obstetrics and Gynaecology Department of the Korle-Bu Teaching Hospital (KBTH) in Accra. Study-relevant information on participants was obtained by means of questionnaire. Vaginal swab samples were collected and processed for laboratory analyses. RESULTS: All the participants (141/141, 100.0 %) indicated they performed intravaginal practices using various methods. Almost half (46.1 %) of these women were between the ages of 25-34 years and 65.0 % were married. Internal douching (82.3 %; p > 0.05) was the commonest practice reported. Other practices such as insertion and wiping with hands and objects, as well as use of locally prepared concoctions and certain commercial products were also reported. The reason most commonly given was for hygienic purpose (83.0 %); a few (10.6 %) did it for sexual satisfaction, while others indicated vaginal tightness (5.7 %) and wound healing (0.7 %) as reasons for their practice. No Lactobacillus sp. was detected in as many as 78.7 % of the sample. Association tests by the Pearson correlation analysis showed strong significant negative correlation (r = -0.954, p < 0.05) between use of traditional herbs/concoction and vaginal lactobacilli colonization; and douching being the least negatively (r = -0.601, p > 0.05) correlated practice. CONCLUSIONS: Vaginal practices were common among the women studied. A more elaborate prospective, case-control study into intravaginal practices and their impact on the health of women in Ghana should be explored.


Assuntos
Lactobacillus , Vagina/microbiologia , Cremes, Espumas e Géis Vaginais/farmacologia , Ducha Vaginal/efeitos adversos , Administração Intravaginal , Adulto , Disbiose/epidemiologia , Disbiose/etiologia , Disbiose/prevenção & controle , Feminino , Gana/epidemiologia , Humanos , Lactobacillus/isolamento & purificação , Lactobacillus/fisiologia , Pessoa de Meia-Idade , Ducha Vaginal/métodos
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