Phylogeography of three closely related African bovids (tribe Alcelaphini). (57/2725)

The phylogeography of three species of African bovids, the hartebeest (Alcelaphus buselaphus), the topi (Damaliscus lunatus), and the wildebeest (Connochaetes taurinus), is inferred from sequence variation of 345 sequences at the control region (d-loop) of the mtDNA. The three species are closely related (tribe Alcelaphini) and share similar habitat requirements. Moreover, their former distribution extended over Africa, as a probable result of the expansion of open grassland on the continent during the last 2.5 Myr. A combination of population genetics (diversity and structure) and intraspecific phylogeny (tree topology and relative branch length) methods is used to substantiate scenarios of the species history. Population dynamics are inferred from the distribution of sequence pairwise differences within populations. In the three species, there is a significant structuring of the populations, as shown by analysis of molecular variance (AMOVA) pairwise and hierarchical differentiation estimations. In the wildebeest, a pattern of colonization from southern Africa toward east Africa is consistent with the asymmetric topology of the gene tree, showing a paraphyletic position of southern lineages, as well as their relatively longer branch lengths, and is supported by a progressive decline in population nucleotide diversity toward east Africa. The phylogenetic pattern found in the topi and the hartebeest differs from that of the wildebeest: lineages split into monophyletic clades, and no geographical trend is detected in population diversity. We suggest a scenario where these antelopes, previously with wide pan-African distributions, became extinct except in a few refugia. The hartebeest, and probably also the topi, survived in refugia north of the equator, in the east and the west, respectively, as well as one in the south. The southern refugium furthermore seems to have been the only place where the wildebeest has survived.  (+info)

Human evolution: the southern route to Asia. (58/2725)

Research on human origins has tended to focus on the origins of western Eurasians; only recently have genetic studies examined south and east Asian populations in depth. Recent work suggests that the supposed Aryan invasion of India 3,000-4,000 years ago was much less significant than is generally believed.  (+info)

HLA and Mooren's ulceration. (59/2725)

BACKGROUND: Mooren's ulcer is a progressive intractable destructive peripheral ulceration of the cornea, probably of autoimmune aetiology. The disease is rare in the northern hemisphere but is more common in southern and central Africa and the Indian subcontinent. Although rare, its predominance in certain racial groups and their second generation migrants worldwide indicates a genetic as well as a geographic predisposition. The highly polymorphic human leucocyte antigens (HLA) confer genetic susceptibility to several autoimmune disorders. Therefore, a possible link between Mooren's ulcer and HLA type was investigated. METHODS: Patients (n=22) with non-infective destructive peripheral corneal inflammatory disease were recruited worldwide. Differential diagnosis confirmed Mooren's ulceration in 12 cases. HLA typing (HLA-A, B, C, DRB, DQB) was performed by serology and PCR using sequence specific primers. The patients came from varied ethnic backgrounds and their HLA typing results were compared with published data from ethnically matched control populations. RESULTS: Of the 12 patients with Mooren's ulcer, 10 (83%) were HLA-DR17(3) positive (including all nine patients of Asian, Indonesian, and black African origin), and 10 (83%) were HLA-DQ2 positive. The frequency of HLA-DR17(3) and DQ2 was higher in the Mooren's ulcer group compared to published data from ethnically matched control populations, where the expected antigen frequencies range between 5% and 40%. CONCLUSION: These results suggest a possible association between HLA-DR17(3) and/or DQ2 and susceptibility to Mooren's ulcer.  (+info)

Preventing mother-to-child transmission of HIV in Africa.(60/2725)

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Survival and progression of HIV disease in women attending GUM/HIV clinics in Britain and Ireland. Study Group for the MRC Collaborative Study of HIV Infection in Women. (61/2725)

OBJECTIVES: To describe the pattern of clinical disease in women with HIV infection and to examine the effect of potential cofactors, including oral contraceptive use, alcohol and smoking, ethnic group, and route of HIV transmission, on progression to AIDS and death. DESIGN: Prospective observational cohort study. SETTING: 15 HIV and genitourinary medicine (GUM) clinics in Britain and Ireland. PARTICIPANTS: 505 women aged over 18 years with a positive HIV antibody test entered the study between June 1992 and August 1995, with outcome data available for 503 women, and 1208 woman years of follow up to April 1996. MAIN OUTCOME MEASURES: AIDS defining conditions, incidence of AIDS, and death. RESULTS: 120 women (24%) had AIDS at entry to the study. There were 99 incident AIDS cases and 132 deaths during 1208 woman years of follow up. Pneumocystis carinii pneumonia (PCP) was the commonest first AIDS defining condition in white women (31% of AIDS cases), followed by oesophageal candidiasis (19%) while tuberculosis was the most common first AIDS defining condition among black African women (24% of AIDS cases), followed by oesophageal candidiasis (19%). In multivariate analyses, rate of progression to AIDS was significantly related to CD4 lymphocyte count at entry and PCP prophylaxis, but not to ethnic group, route of HIV transmission, alcohol, smoking, or oral contraceptive use. Mortality from all causes was not significantly different in women infected through injecting drugs (adjusted ratio 1.1, 95% confidence interval 0.7-1.8) compared with those infected through sexual intercourse, and non-significantly lower in black African women (0.7, 0.3-1.2) compared with white women. Survival was not significantly related to smoking, alcohol, or oral contraceptive use. CONCLUSIONS: In women attending GUM/HIV clinics, the pattern of AIDS defining conditions differs by ethnic group, but progression of HIV disease is not importantly related to smoking, alcohol, oral contraceptive use, route of HIV transmission, or ethnic group.  (+info)

Incidence of gonorrhoea diagnosed in GUM clinics in South Thames (west) region. (62/2725)

OBJECTIVES: To describe the incidence of gonorrhoea diagnosed in genitourinary medicine (GUM) clinics in South Thames (West) between 1995 and 1996, and how it changed among population subgroups. SETTINGS AND SUBJECTS: Cases of uncomplicated and complicated gonorrhoea diagnosed at 13 GUM clinics in the former South Thames West (STW) Regional Health Authority that reported disaggregate data to the South Thames GUM Clinic Collaborative STD Surveillance Scheme. METHODS: Annual incidence rates (per 100,000) of gonorrhoea diagnoses by sex, age group, ethnic group, area of residence, and year were calculated. Poisson regression models were used to calculate risk ratios (RR) to describe the key differences in the variation of gonorrhoea cases by these variables. Relative differences in the incidence of diagnosed gonorrhoea between 1995 and 1996 were investigated by including an interaction between year and the other variables (age group, sex, ethnic group, region) and testing whether any were significant using a likelihood ratio test. RESULTS: Area of residence, sex, age group, and ethnic group were key predictors of the rates of diagnosed gonorrhoea. The risk ratio for gonorrhoea (after adjustment for the other variables) was: 13 times higher among blacks than the white population; twice as high in inner London compared with outer London; and three times lower in the "shire" region compared with outer London. The rate of diagnosed gonorrhoea was significantly higher in the black population in the shire region than the inner London white population. The rate of gonorrhoea diagnosed by GUM clinics from 1995 to 1996 almost doubled in the white population aged 15-44 years, from 16 cases per 100,000 to 30 cases per 100,000 (adjusted RR 2.0, 95% CI 1.6 to 2.4), whereas increased rates in the black and Asian/other ethnic groups were not statistically significant (adjusted RR 1.1, 95% CI 0.9 to 1.4; and 1.4, 95% CI 0.7 to 2.7 respectively). CONCLUSION: The observed increase in gonorrhoea between 1995 and 1996 occurred mostly among heterosexual white men and women. Overall, the rates of gonorrhoea among young people, especially in the black population and in inner London represent a significant public health problem that may merit further targeted interventions, the effectiveness of which could be monitored through further development of routine surveillance data.  (+info)

Re-emergence of Chikungunya and O'nyong-nyong viruses: evidence for distinct geographical lineages and distant evolutionary relationships. (63/2725)

Chikungunya (CHIK) virus is a member of the genus Alphavirus in the family TOGAVIRIDAE: Serologically, it is most closely related to o'nyong-nyong (ONN) virus and is a member of the Semliki Forest antigenic complex. CHIK virus is believed to be enzootic throughout much of Africa and historical evidence indicates that it spread to other parts of the world from this origin. Strains from Africa and Asia are reported to differ biologically, indicating that distinct lineages may exist. To examine the relatedness of CHIK and ONN viruses using genetic data, we conducted phylogenetic studies on isolates obtained throughout Africa and Southeast Asia. Analyses revealed that ONN virus is indeed distinct from CHIK viruses, and these viruses probably diverged thousands of years ago. Two distinct CHIK virus lineages were delineated, one containing all isolates from western Africa and the second comprising all southern and East African strains, as well as isolates from Asia. Phylogenetic trees corroborated historical evidence that CHIK virus originated in Africa and subsequently was introduced into Asia. Within the eastern Africa and southern Africa/Asia lineage, Asian strains grouped together in a genotype distinct from the African groups. These different geographical genotypes exhibit differences in their transmission cycles: in Asia, the virus appears to be maintained in an urban cycle with Aedes aegypti mosquito vectors, while CHIK virus transmission in Africa involves a sylvatic cycle, primarily with AE: furcifer and AE: africanus mosquitoes.  (+info)

Spread of distinct human immunodeficiency virus type 1 AG recombinant lineages in Africa. (64/2725)

To identify new subtype G human immunodeficiency virus type 1 (HIV-1) strains and AG recombinant forms, we collected 28 serum samples from immigrants to the Netherlands from 12 countries throughout Africa. Based on the gag sequences 22 isolates were identified as subtype A or G. Phylogenetic analysis of discontinuous regions of the gag (726 nt), pol (1176 nt) and env (276 nt) genes revealed 13 AG recombinants with the mosaic structure A(gag)/G(pol)/A(env), three with A(gag)/G(pol)/G(env) and one other with A(gag) /G(pol)/G(env), in addition to 'pure' subtypes A(gag)/A(pol)/A(env) (n=1) and G(gag)/G(pol)/G(env) (n=4). To analyse the crossover points in more detail, a new RT-PCR was developed resulting in a large contiguous sequence of 2600 nt from the gag region to half the pol region. All the 13 A(gag)/G(pol)/A(env) recombinants appeared to belong to the circulating recombinant form (CRF) AG (IbNG). The three A(gag)/G(pol) /G(env) recombinants differed from the CRF AG (IbNG) subtype, suggesting the identification of a new CRF subtype. The recovery of AG recombinants from African countries a thousand miles apart indicates the active spread of new recombinants.  (+info)