Dataset Information

Epidemic history and evolutionary dynamics of hepatitis B virus infection in two remote communities in rural Nigeria.

ABSTRACT: BACKGROUND: In Nigeria, hepatitis B virus (HBV) infection has reached hyperendemic levels and its nature and origin have been described as a puzzle. In this study, we investigated the molecular epidemiology and epidemic history of HBV infection in two semi-isolated rural communities in North/Central Nigeria. It was expected that only a few, if any, HBV strains could have been introduced and effectively transmitted among these residents, reflecting limited contacts of these communities with the general population in the country. METHODS AND FINDINGS: Despite remoteness and isolation, approximately 11% of the entire population in these communities was HBV-DNA seropositive. Analyses of the S-gene sequences obtained from 55 HBV-seropositive individuals showed the circulation of 37 distinct HBV variants. These HBV isolates belong predominantly to genotype E (HBV/E) (n=53, 96.4%), with only 2 classified as sub-genotype A3 (HBV/A3). Phylogenetic analysis showed extensive intermixing between HBV/E variants identified in these communities and different countries in Africa. Quasispecies analysis of 22 HBV/E strains using end-point limiting-dilution real-time PCR, sequencing and median joining networks showed extensive intra-host heterogeneity and inter-host variant sharing. To investigate events that resulted in such remarkable HBV/E diversity, HBV full-size genome sequences were obtained from 47 HBV/E infected persons and P gene was subjected to Bayesian coalescent analysis. The time to the most recent common ancestor (tMRCA) for these HBV/E variants was estimated to be year 1952 (95% highest posterior density (95% HPD): 1927-1970). Using additional HBV/E sequences from other African countries, the tMRCA was estimated to be year 1948 (95% HPD: 1924-1966), indicating that HBV/E in these remote communities has a similar time of origin with multiple HBV/E variants broadly circulating in West/Central Africa. Phylogenetic analysis and statistical neutrality tests suggested rapid HBV/E population expansion. Additionally, skyline plot analysis showed an increase in the size of the HBV/E-infected population over the last approximately 30-40 years. CONCLUSIONS: Our data suggest a massive introduction and relatively recent HBV/E expansion in the human population in Africa. Collectively, these data show a significant shift in the HBV/E epidemic dynamics in Africa over the last century.

SUBMITTER: Forbi JC

PROVIDER: S-EPMC2906510 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Epidemic history and evolutionary dynamics of hepatitis B virus infection in two remote communities in rural Nigeria.

Forbi Joseph C JC Vaughan Gilberto G Purdy Michael A MA Campo David S DS Xia Guo-liang GL Ganova-Raeva Lilia M LM Ramachandran Sumathi S Thai Hong H Khudyakov Yury E YE

PloS one 20100719 7

<h4>Background</h4>In Nigeria, hepatitis B virus (HBV) infection has reached hyperendemic levels and its nature and origin have been described as a puzzle. In this study, we investigated the molecular epidemiology and epidemic history of HBV infection in two semi-isolated rural communities in North/Central Nigeria. It was expected that only a few, if any, HBV strains could have been introduced and effectively transmitted among these residents, reflecting limited contacts of these communities wit ...[more]

PMID: 20657838

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Project description:BackgroundHepatitis E virus (HEV) is an enterically transmitted hepatropic virus. It segregates as four genotypes. All genotypes infect humans while only genotypes 3 and 4 also infect several animal species. It has been suggested that hepatitis E is zoonotic, but no study has analyzed the evolutionary history of HEV. We present here an analysis of the evolutionary history of HEV.Methods and findingsThe times to the most recent common ancestors for all four genotypes of HEV were calculated using BEAST to conduct a Bayesian analysis of HEV. The population dynamics for genotypes 1, 3 and 4 were analyzed using skyline plots. Bayesian analysis showed that the most recent common ancestor for modern HEV existed between 536 and 1344 years ago. The progenitor of HEV appears to have given rise to anthropotropic and enzootic forms of HEV, which evolved into genotypes 1 and 2 and genotypes 3 and 4, respectively. Population dynamics suggest that genotypes 1, 3 and 4 experienced a population expansion during the 20(th) century. Genotype 1 has increased in infected population size ∼30-35 years ago. Genotype 3 and 4 have experienced an increase in population size starting late in the 19(th) century until ca.1940-45, with genotype 3 having undergone additional rapid expansion until ca.1960. The effective population size for both genotype 3 and 4 rapidly declined to pre-expansion levels starting in ca.1990. Genotype 4 was further examined as Chinese and Japanese sequences, which exhibited different population dynamics, suggesting that this genotype experienced different evolutionary history in these two countries.ConclusionsHEV appears to have evolved through a series of steps, in which the ancestors of HEV may have adapted to a succession of animal hosts leading to humans. Analysis of the population dynamics of HEV suggests a substantial temporal variation in the rate of transmission among HEV genotypes in different geographic regions late in the 20(th) Century.

Project description:Different explanations exist on how HIV-1 subtype B spread in Central America, but the role of Guatemala, the Central American country with the highest number of people living with the virus, in this scenario is unknown. We investigated the evolutionary history and spatiotemporal dynamics of HIV-1 subtype B in Guatemala. A total of 1,047 HIV-1 subtype B pol sequences, from newly diagnosed ART-naïve, HIV-infected Guatemalan subjects enrolled between 2011 and 2013 were combined with published subtype B sequences from other Central American countries (n = 2,101) and with reference sequences representative of the BPANDEMIC and BCAR lineages from the United States (n = 465), France (n = 344) and the Caribbean (n = 238). Estimates of evolutionary, demographic, and phylogeographic parameters were obtained from sequence data using maximum likelihood and Bayesian coalescent-based methods. The majority of Guatemalan sequences (98.9%) belonged to the BPANDEMIC clade, and 75.2% of these sequences branched within 10 monophyletic clades: four also included sequences from other Central American countries (BCAM-I to BCAM-IV) and six were mostly (>99%) composed by Guatemalan sequences (BGU clades). Most clades mainly comprised sequences from heterosexual individuals. Bayesian coalescent-based analyses suggested that BGU clades originated during the 1990s and 2000s, whereas BCAM clades originated between the late 1970s and mid 1980s. The major hub of dissemination of all BGU, and of BCAM-II, and BCAM-IV clades was traced to the Department of Guatemala, while the root location of BCAM-I and BCAM-III was traced to Honduras. Most Guatemalan clades experienced initial phases of exponential growth (0.23 and 3.6 year-1), followed by recent growth declines. Our observations suggest that the Guatemalan HIV-1 subtype B epidemic is driven by dissemination of multiple BPANDEMIC founder viral strains, some restricted to Guatemala and others widely disseminated in the Central American region, with Guatemala City identified as a major hub of viral dissemination. Our results also suggest the existence of different sub-epidemics within Guatemala for which different targeted prevention efforts might be needed.

Project description:BackgroundIn Canada, as in other parts of the world, there is geographic maldistribution of the nursing workforce, and insufficient attention is paid to the strengths and needs of those providing care in rural and remote settings. In order to inform workforce planning, a national study, Nursing Practice in Rural and Remote Canada II, was conducted with the rural and remote regulated nursing workforce (registered nurses, nurse practitioners, licensed or registered practical nurses, and registered psychiatric nurses) with the intent of informing policy and planning about improving nursing services and access to care. In this article, the study methods are described along with an examination of the characteristics of the rural and remote nursing workforce with a focus on important variations among nurse types and regions.MethodsA cross-sectional survey used a mailed questionnaire with persistent follow-up to achieve a stratified systematic sample of 3822 regulated nurses from all provinces and territories, living outside of the commuting zones of large urban centers and in the north of Canada.ResultsRural workforce characteristics reported here suggest the persistence of key characteristics noted in a previous Canada-wide survey of rural registered nurses (2001-2002), namely the aging of the rural nursing workforce, the growth in baccalaureate education for registered nurses, and increasing casualization. Two thirds of the nurses grew up in a community of under 10 000 people. While nurses' levels of satisfaction with their nursing practice and community are generally high, significant variations were noted by nurse type. Nurses reported coming to rural communities to work for reasons of location, interest in the practice setting, and income, and staying for similar reasons. Important variations were noted by nurse type and region.ConclusionsThe proportion of the rural nursing workforce in Canada is continuing to decline in relation to the proportion of the Canadian population in rural and remote settings. Survey results about the characteristics and practice of the various types of nurses can support workforce planning to improve nursing services and access to care.

Dataset Information

Epidemic history and evolutionary dynamics of hepatitis B virus infection in two remote communities in rural Nigeria.

Publications

Epidemic history and evolutionary dynamics of hepatitis B virus infection in two remote communities in rural Nigeria.

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