scholarly journals A4 An amplicon-based approach for universal amplification, sequencing, and assembly of full-length HIV-1 samples from the DRC

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
M Bletsa ◽  
N Vidal ◽  
B Vrancken ◽  
S Lequime ◽  
M Peeters ◽  
...  
Keyword(s):  
Complete Genome ◽  
Democratic Republic Of Congo ◽  
Central Africa ◽  
Human Populations ◽  
Genome Data ◽  
Sequencing Method ◽  
History Of ◽  
Key Aspects ◽  
Traditional Approaches ◽  
Hiv 1

Abstract Phylogenetic studies have contributed to our understanding of the early epidemic onset of HIV-1 in the Democratic Republic of Congo (DRC); however, the factors driving its early emergence and establishment in human populations still remain unresolved. In order to determine the key aspects of its successful epidemic spread, complete genome data are required from samples representative of the viral diversity in the DRC. In this study, we have established a universal PCR-assay that uses seven different panels of primers to produce overlapping amplicons covering the complete HIV genome. To circumvent the limitations of purifying these fragments and sequencing them with traditional approaches, we have developed a massive parallel sequencing method and a protocol for efficiently assembling HIV-1 genomes. A total of thirty-six samples, collected between 1997 and 2001 from different locations across the DRC, have been obtained, and, at this stage, we are focusing on complementing our dataset with more archival samples that can be used as HIV ‘molecular fossils’. By generating complete genome phylogeographic data from the DRC, we aim to create a genomic window into the past evolutionary and epidemiological dynamics of HIV-1 in Central Africa and understand the natural history of this devastating pandemic.

scholarly journals The early spread and epidemic ignition of HIV-1 in human populations

Science ◽  
2014 ◽  
Vol 346 (6205) ◽  
pp. 56-61 ◽  
Author(s):  
Nuno R. Faria ◽  
Andrew Rambaut ◽  
Marc A. Suchard ◽  
Guy Baele ◽  
Trevor Bedford ◽  
...  
Keyword(s):  
Democratic Republic ◽  
Democratic Republic Of Congo ◽  
Sequence Data ◽  
Central Africa ◽  
Human Populations ◽  
Social Changes ◽  
Transport Networks ◽  
Regional Population ◽  
Hiv 1

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

Revealing the history of infectious disease epidemics through phylogenetic trees

1995 ◽  
Vol 349 (1327) ◽  
pp. 33-40 ◽  
Keyword(s):  
Phylogenetic Trees ◽  
Viral Transmission ◽  
Human Populations ◽  
Viral Sequence ◽  
Immunodeficiency Virus ◽  
History Of ◽  
The Difference ◽  
Disease Epidemics ◽  
Hiv 1

Phylogenetic trees play an increasing role in molecular epidemiology, where they have been used to understand the forces that shape patterns of viral sequence diversity. Phylogenetic trees can also be used to trace the dynamics of viral transmission within populations. Case studies document the worldwide spread of Human Immunodeficiency Virus type 1 (HIV -1) and hepatitis C virus (HCV). Despite similarities between these viruses, especially in their transmission routes, they are shown to have very different epidemiological histories. A possible reason for the difference is that HCV has coexisted longer with human populations.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

2019 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

AbstractGenome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

scholarly journals Origin of the HIV-1 group O epidemic in western lowland gorillas

2015 ◽  
Vol 112 (11) ◽  
pp. E1343-E1352 ◽  
Author(s):  
Mirela D’arc ◽  
Ahidjo Ayouba ◽  
Amandine Esteban ◽  
Gerald H. Learn ◽  
Vanina Boué ◽  
...  
Keyword(s):  
Democratic Republic Of Congo ◽  
Cytidine Deaminase ◽  
Virus Transmission ◽  
Central Africa ◽  
Source Population ◽  
Human Virus ◽  
Southern Cameroon ◽  
Western Lowland Gorillas ◽  
Hiv 1 ◽  
Lowland Gorillas

HIV-1, the cause of AIDS, is composed of four phylogenetic lineages, groups M, N, O, and P, each of which resulted from an independent cross-species transmission event of simian immunodeficiency viruses (SIVs) infecting African apes. Although groups M and N have been traced to geographically distinct chimpanzee communities in southern Cameroon, the reservoirs of groups O and P remain unknown. Here, we screened fecal samples from western lowland (n= 2,611), eastern lowland (n= 103), and mountain (n= 218) gorillas for gorilla SIV (SIVgor) antibodies and nucleic acids. Despite testing wild troops throughout southern Cameroon (n= 14), northern Gabon (n= 16), the Democratic Republic of Congo (n= 2), and Uganda (n= 1), SIVgor was identified at only four sites in southern Cameroon, with prevalences ranging from 0.8–22%. Amplification of partial and full-length SIVgor sequences revealed extensive genetic diversity, but all SIVgor strains were derived from a single lineage within the chimpanzee SIV (SIVcpz) radiation. Two fully sequenced gorilla viruses from southwestern Cameroon were very closely related to, and likely represent the source population of, HIV-1 group P. Most of the genome of a third SIVgor strain, from central Cameroon, was very closely related to HIV-1 group O, again pointing to gorillas as the immediate source. Functional analyses identified the cytidine deaminase APOBEC3G as a barrier for chimpanzee-to-gorilla, but not gorilla-to-human, virus transmission. These data indicate that HIV-1 group O, which spreads epidemically in west central Africa and is estimated to have infected around 100,000 people, originated by cross-species transmission from western lowland gorillas.

scholarly journals Genomic history of human monkey pox infections in the Central African Republic between 2001 and 2018

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Berthet ◽  
Stéphane Descorps-Declère ◽  
Camille Besombes ◽  
Manon Curaudeau ◽  
Andriniaina Andy Nkili Meyong ◽  
...  
Keyword(s):  
Central African Republic ◽  
Democratic Republic Of Congo ◽  
Central Africa ◽  
Armed Conflicts ◽  
Molecular Dating ◽  
Congo Basin ◽  
Wild Animals ◽  
Population Movements ◽  
History Of ◽  
Northern Edge

AbstractMonkeypox is an emerging infectious disease, which has a clinical presentation similar to smallpox. In the two past decades, Central Africa has seen an increase in the frequency of cases, with many monkeypox virus (MPXV) isolates detected in the Democratic Republic of Congo (DRC) and the Central African Republic (CAR). To date, no complete MPXV viral genome has been published from the human cases identified in the CAR. The objective of this study was to sequence the full genome of 10 MPXV isolates collected during the CAR epidemics between 2001 and 2018 in order to determine their phylogenetic relationships among MPXV lineages previously described in Central Africa and West Africa. Our phylogenetic results indicate that the 10 CAR isolates belong to three lineages closely related to those found in DRC. The phylogenetic pattern shows that all of them emerged in the rainforest block of the Congo Basin. Since most human index cases in CAR occurred at the northern edge of western and eastern rainforests, transmissions from wild animals living in the rainforest is the most probable hypothesis. In addition, molecular dating estimates suggest that periods of intense political instability resulting in population movements within the country often associated also with increased poverty may have led to more frequent contact with host wild animals. The CAR socio-economic situation, armed conflicts and ecological disturbances will likely incite populations to interact more and more with wild animals and thus increase the risk of zoonotic spillover.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

Science ◽  
2020 ◽  
Vol 367 (6484) ◽  
pp. eaay5012 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

scholarly journals Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Xingguang Li ◽  
Haizhou Liu ◽  
Lu Liu ◽  
Yi Feng ◽  
Marcia L. Kalish ◽  
...  
Keyword(s):  
Complete Genome ◽  
Genome Sequences ◽  
History Of ◽  
Hiv 1

scholarly journals Understanding the possible origin and genotyping of first Bangladeshi SARS-CoV-2 strain

2020 ◽  
Author(s):  
A. S. M. Rubayet Ul Alam ◽  
M. Rafiul Islam ◽  
M. Shaminur Rahman ◽  
Ovinu Kibria Islam ◽  
M. Anwar Hossain
Keyword(s):  
Complete Genome ◽  
Epidemiological Data ◽  
The Novel ◽  
Genome Data ◽  
The United Kingdom ◽  
Comprehensive Picture ◽  
History Of ◽  
Probable Origin ◽  
Novel Coronavirus ◽  
The Uk

The novel coronavirus, SARS-CoV-2, causes the unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen, the first complete genome of the virus has very recently been published. Therefore, the long awaiting questions regarding the possible origin and typing of the strain(s) can now be answered. Here, we endeavor to mainly discuss the published reports or online-accessed data (results) regarding those issues and presented a comprehensive picture of the typing of the virus alongside the probable origin of the sub-clade containing Bangladeshi strain. Our observation suggested that this strain might have originated from the United Kingdom (UK) or other European countries epidemiologically linked to the UK. According to different genotyping classification schemes, this strain belongs to A2a clade under G major clade, is of B and/or L type, and is a SARS-CoV-2a sub-strain. The complete genome data will surely increase in the forwarding days in Bangladesh. However, a mass regional sequencing approach targeting the partial or complete genome can link the epidemiological data and may help in further clinical interventions.

scholarly journals Uma coleção-documento: estudo da coleção de cópias em gesso de arte centro-africana do Museu Afro-Brasileiro-UFBA- primeiras notícias de pesquisa

2017 ◽  
Author(s):  
Joseania Freitas
Keyword(s):  
Democratic Republic Of Congo ◽  
Central Africa ◽  
African Art ◽  
Art Collections ◽  
Doctoral Research ◽  
North East ◽  
The North ◽  
Ethnographic Museums ◽  
History Of ◽  
Study Process

This post-doctoral research deals with the study of a collection of twelve copies of important works to act as a reference of the Center African Art, highlighted in the main specialized books and catalogs. Copies belong to the Afro-Brazilian Museum collection of the Federal University of Bahia (MAFRO / UFBA), were donated by the Royal Museum of Central Africa (Tervuren, Belgium). To understand the trajectory and the history of this collection of plaster copies, like collection-document, we had to work with institutional and personal stories, and live with lacunars spaces of the various files. This museum plot refers to the background of the creation of the great ethnographic museums, since the trajectory of the copies does not dissociate the trajectory of their original. The original pieces were taken from the former Belgian Congo, with productions of people in the geographic regions of the Democratic Republic of Congo and the North East of Angola. The colonial-slavery history, with its institutions and characters, is intertwined with parts in different contexts, since the withdrawal of their places of origin, nullifying their functions and uses, processing in ethnographic collections and later in art collections, serving material support for the dissemination of racial and racist ideas of cultural and social inferiority of African people. It is intended, at the end of the study process, produce a written narrative with several voices (book and catalog) and a expographic narrative, which will deal with matters relating to the implications and intertwining of stories involving the original collection and prints, different individuals and institutions that are particularly marked by their identity characteristics. Keywords: art central African, memory, patrimony, museums.

scholarly journals Fishes of the Kwilu River (Kasai basin, central Africa): A list of species collected in the vicinity of Kikwit, Bandundu Province, Democratic Republic of Congo

Check List ◽  
2011 ◽  
Vol 7 (5) ◽  
pp. 691 ◽  
Author(s):  
José Justin Mbimbi Mayi Munene ◽  
Melanie L. J. Stiassny
Keyword(s):  
Democratic Republic ◽  
Democratic Republic Of Congo ◽  
Central Africa ◽  
Congo Basin ◽  
Left Bank ◽  
Republic Of Congo ◽  
Biogeographic History ◽  
Starting Point ◽  
History Of ◽  
Distributional Knowledge

A list of fishes collected in the vicinity of Kikwit on the Kwilu River, a large left bank tributary of the Kasai River in the Democratic Republic of Congo is provided. One hundred and thirteen species distributed in 21 families are reported, and of these 29 species are recognized as representing new records for the region. Lack of up-to-date taxonomic and distributional knowledge of African fishes, a problem particularly acute in the central Congo basin, is clearly reflected in this high number of range extensions. While preliminary, this contribution serves as a useful starting point for efforts to understand the ichthyofaunal composition and biogeographic history of the Kasai system; one of the most poorly documented river systems in central Africa.

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