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PubMed1995

The availability of health information in South Africa.

The South African Medical Research Council (MRC) has provided access to on-line health and biomedical information since 1976, when the MRC became an international partner of NLM. This was done to support research and health care when the Institute of Biomedical Communication was established. The institute has since reorganized and is now the Information Systems Division in the Research Systems Support Group MRC. he MRC and medical libraries in South Africa are able to access various automated services via telecommunication. The major systems available are MEDLARS, DIALOG, DATASTAR and BRS, with ECRI being the latest addition; most used are MEDLARS and DIALOG. New technologies (e.g., CD-ROM) have given more people access. This technology is not available to many people working in Primary Health Care (PHC), as they do not have access to computer networks. Beyond on-line is statistical and printed information, called "Gray Literature," not accessible through on-line systems as it is not published in conventional sources used to build databases. With a shift to Essential National Health Research and the focus on PHC and preventative medicine, demand for health information and "gray literature" is growing. The MRC collects and produces this material and has its own database called SAMED, which is to be made available to others as our contribution to health. It is hoped to make this available for inclusion in the proposed African Index Medicus presently investigated by the World Health Organization. Africa as a continent, and South Africa as a country, are experiencing major changes in health care and medical practice, and inevitably, provision of health information services. With South Africa's re-entry into the global village and its acceptance by the rest of Africa, it can be a key player in information provision to the rest of the continent. The MRC, as a major provider of Health information, can play a vital role in the information flow throughout Africa by continuously improving and expanding its services. A large proportion of South Africans live in rural areas where health care is provided by clinics not linked to information networks. This does not mean these clinics are excluded from the use of information. The major challenge is to find the ways and means of getting the relevant information to these clinics. Information is needed to help with patient care and continuing education. With this in mind, the MRC is evaluating different formats in which information can be supplied. Due to the lack of computer literacy, facilities, and financial constraints, it is better to supply printed information. With the spread of technology through the country and continent, it can be assumed that information flow and transfer will be more rapid. Repackaging of information means that it is possible to get the relevant information to the right people at the right time. The first such package developed is for hospital managers. With the help from experts in the field of PHC, it is hoped to develop packages aimed specifically at the CHWs and other workers in the field. All packages developed by the MRC are backed by a document provision service, using the most cost-effective route to obtain documents. A printed product must comply with certain criteria; these are: 1) purpose for which the information is needed; 2) kind of information needed and the format in which it is needed; 3) when the information is needed; 4) is the information to be supplied on an ongoing basis i.e., updated with latest information; 5) cost involved; and 6) how to get the information to the relevant user.

Computer Communication Networks↗
PubMed1996

Disasters in Africa: old and new hazards and growing vulnerability.

Disasters occur when hazards and vulnerability meet. Out of 100 disasters reported worldwide, only 20 occur in Africa, but Africa suffers 60% of all disaster-related deaths. This is probably due to the type of hazards that affect this continent, to under-reporting, and to the fact that under the circumstances prevailing in Africa, it is easy for any disaster to escalate and multiply its impact. Africa's natural hazards are mainly epidemics, endemic diseases, drought, floods, agricultural pests and bush fires, but some areas are also susceptible to earthquakes, cyclones and volcanic eruptions. The natural hazards interact with manmade ones, such as armed conflicts, air, road and railway incidents, other industrial hazards such as mining accidents, chemical spills, etc., and with widespread vulnerability. The context is one of rapid population growth, forced movements of population, environmental degradation, precarious urbanization, food insecurity, poverty, fragile economies, infrastructures and institutions, and cultural and political instability. The 53 countries of the continent are highly susceptible and vulnerable and their 761,390,000 people are exposed to both natural and manmade hazards. Through complex causal chains, disasters affect people directly and indirectly. In the first 6 months of 1996, meningitis had already killed 5,000 people. Throughout Africa, there are 500,000 measles-associated deaths each year; the direct and indirect costs of malaria are estimated at US$ 1.7 billion per year. In June 1996 food emergencies were looming in 14 African countries with 22 million people facing direct food shortages. Since 1980, conflicts have caused at least 3.7 million excess deaths and cost the Region about US$ 13 billion per year. Wars have destroyed 70% of the health network of some countries, and have left behind 30-40 million landmines, making Africa the most mine-infested continent in the world.

Africa↗
PubMed1993

Soap and water prophylaxis for limiting genital ulcer disease and HIV-1 infection in men in sub-Saharan Africa.

In general, East, Central and Southern Africa appear to be worse affected by HIV-1 infection than West Africa. So far there is little evidence to suggest that differences in either sexual behaviour or numbers of sexual partners could account for this disparity. Two risk factors in men for acquiring HIV-1, that tend to vary along this geographical divide, are lack of circumcision and genital ulcer disease (GUD) which are much less common in West Africa. Although uncircumcised men with GUD are an important high frequency HIV-1 transmitter core group, few interventions have targeted such individuals. Given the recent expansion in AIDS-related technologies, is it possible that methods effective in limiting GUD in the preantibiotic era have been overlooked? During the first and second world wars, chancroid, the commonest cause of GUD in Africa today, was controlled successfully with various prophylactics including soap and water. Many parts of Africa are undergoing social upheaval against a background of violence, and in this environment soap and water prophylaxis would now seem to merit re-evaluation as an intervention for preventing both GUD and HIV-1 in uncircumcised men. By facilitating healing of traumatic, inflammatory and infected penile lesions, pre- and post-exposure prophylaxis with soap and water could be a cheap and effective method for decreasing the risks of acquiring GUD and HIV in this vulnerable group of uncircumcised men.

Africa South of the Sahara↗
PubMed1999

Lest the rhetoric begin: migration, population and the environment in Southern Africa.

In the spirited debate over cross-border migration in southern Africa there is one issue that has been conspicuously absent: the environment. The issue is raised in this article not because it necessarily deserves to be part of the debate--it will be argued, in fact that one needs to tread very carefully when drawing any linkages between migration and the environment--but because it has received an inordinate amount of attention in the academic and popular press in other parts of the world (particularly in the US) and could influence South African immigration policy and debates. In this article the authors look specifically at Thomas Homer-Dixon's influential work on environmental scarcity and migration and critically assess its relevance in the southern African context. A brief review of the history of migration and immigration policy in the region is followed by a theoretical and empirical critique of Homer Dixon's writings. It is acknowledged in the article that environmental degradation can (and does) contribute to forced migration and violent conflict in southern Africa, but it is also argued that Homer-Dixon misses some fundamental points about the political economy of (post) apartheid southern Africa and in doing so presents a very problematic interpretation of the causes and effects of migration in the region. The potential for these theories to lend themselves to a reactionary, closed-border approach to immigration in South Africa is also discussed and forms part of the impetus for the writing of this paper.

Africa↗
PubMed1997

Emergent migration policy in a democratic South Africa.

This article sets recent debates on migration policy in South Africa against broader historical realities that have shaped patterns of population movement on the subcontinent since the end of the nineteenth century. During the course of the last century, most forms of population movement were the result of disjointed regional economic development which can be traced to two epochal events at the end of the nineteenth century: the creation of the modern African state system and the discovery of mineral wealth in Southern Africa. Although regulation of migrant labor was a fundamental feature of the colonial period, it was only after 1950, when independent states began to define specific migration priorities, that states began to restrict significantly the flow of transnational labor. From this point notions such as internally displaced person, refugee and illegal immigrant become increasingly appropriate to the study of regional migration. Particular attention is given to current debate on the definition of refugee which forms part of a broader international debate. A number of South African writers have argued that, given the structural imbalances contained in the regional economy, the term "refugee" should be redefined to included economic migrants. This position is not shared by the South African Government, and an analysis of current policy and legislation demonstrates a growing tendency to restrict the influx of undocumented migrants. This is due, in part, to the recent political transition and the institutional compromises that it produced as well as the growth of negative sentiment towards illegal immigrants at both mass and elite levels, as demonstrated by two recent research findings. The article concludes with a summation of recent trends in South African migration policy and an evaluation of the ambiguous position that South Africa occupies within Southern Africa.

Africa↗
PubMed2022

Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa.

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa.

Africa, Southern↗
PubMed2003

The emergence of Taenia solium cysticercosis in Eastern and Southern Africa as a serious agricultural problem and public health risk.

Pig production has increased significantly in the Eastern and Southern Africa (ESA) region during the past decade, especially in rural, resource-poor, smallholder communities. Concurrent with the increase in smallholder pig keeping and pork consumption, there have been increasing reports of porcine cysticercosis in the ESA region. This article reviews the findings concerning the presence and impact of porcine cysticercosis in seven of the ESA countries. Most of the reported findings are based on surveys utilising lingual palpation and post-mortem examination, however, some also used serological assays. In Tanzania, community-based studies on porcine cysticercosis indicate a prevalence of 17.4% in the northern highlands district of Mbulu and a prevalence range of 5.1-16.9% in the southern highlands. In Kenya recent surveys in the southwestern part of the country where smallholder pig keeping is popular indicate that 10-14% of pigs are positive for cysticercosis by lingual examination. Uganda has the most pigs in Eastern Africa, most of which are kept under smallholder conditions. Preliminary surveys in 1998 and 1999 at slaughterhouses in Kampala indicated a prevalence of porcine cysticercosis between 0.12 and 1.2%, however, a rural survey in northern Uganda in 1999 indicated 34-45% of pigs slaughtered in selected villages were infected. Additionally, a new survey of 297 pigs slaughtered in Kampala in 2002 indicated that pigs from the central region of the country were negative for cysticercosis while 33.7% of the pigs coming from the rural Lira district in the north were positive. Interestingly 8 piglet foetuses removed from an infected slaughtered sow coming from Lira district were all found to harbour cysts of T. solium providing evidence of congenital transmission of porcine cysticercosis. In Mozambique, abattoir records indicate that porcine cysticercosis is present in all provinces of the country. A serological survey on pigs in rural Tete Province found 15% of pigs positive. In Zimbabwe, a retrospective study in official abattoirs around the country from 1994 to 2001 reported a mean prevalence of 0.34% which is in contrast to a post-mortem survey in 1999, which showed that the prevalence of porcine cysticercosis in rural west Zimbabwe where smallholder pig keeping is popular was 28.6%. In Zambia, abattoir records reported porcine cysticercosis in six of the nine provinces. Routine meat inspection of 1316 pigs at a slaughter slab in Lusaka showed that 20.6% of the pigs had cysticercosis whereas serological testing of 874 pigs at the same abattoir indicated that 56.6% were found to have circulating antigens of Taenia solium. Field surveys based on lingual palpation in Southern and Eastern Provinces of Zambia revealed prevalences of 8.2-28.4 and 5.2%, respectively. South Africa has the largest number of pigs in Southern Africa and cysticercosis has been recognised as a problem in the country for many decades. There is strong evidence supporting the high prevalence of neurocysticercosis infecting humans from resource-poor areas of the country where pigs are being raised under smallholder conditions. In spite of this community-based surveys on porcine cysticercosis have never been conducted in South Africa and the last slaughterhouse survey was conducted nearly 40 years ago. The prevalences of porcine cysticercosis found in these ESA countries rank among the highest in the world and the disease is emerging as an important constraint for the nutritional and economic well being of resource-poor smallholder farming communities. The current findings suggest the widespread presence of human tapeworm carriers and thus a high risk of human cysticercosis in both rural areas and urban centres in the ESA region. More research is required in the region to assess the extent and public health and economic impact of T. solium infection in order to determine whether and what prevention and control efforts are needed.

Abattoirs↗
PubMed1985

Recent trends in the importation of malaria caused by Plasmodium falciparum into the United States from Africa.

National malaria surveillance data were reviewed in an analysis of the epidemiological impact of the transmission of chloroquine-resistant Plasmodium falciparum in Africa on malaria in the United States. Between 1975 and 1983, P. falciparum infections acquired by U.S. citizens who visited East Africa, especially Kenya, increased 21-fold. Estimated attack rates for P. falciparum per 100,000 U.S. travelers to Kenya rose from 21.2 cases in 1977 to 83.3 cases in 1982, a rise suggesting that the increase in imported malaria was not due to increased travel. The percentage of reported cases in U.S. citizens with P. falciparum infections acquired in East Africa who indicated having used chloroquine prophylaxis increased from 22.2% in 1978 to 75.8% in 1983; in contrast, no change in the reported use of chloroquine prophylaxis was observed in those infected in West Africa during the same period. These results suggest that chloroquine can no longer be considered a highly effective drug for prevention of malaria caused by P. falciparum in U.S. travelers to East Africa.

Africa, Eastern↗
PubMed1999

Plague epidemiology and control in eastern and southern Africa during the period 1978 to 1997.

Human plague is one of the important re-emerging zoonotic diseases threatening public health in some African, Asian and South American countries. During the period 1978 to 1997, Africa reported the largest numbers of plague cases and deaths in the world. During the decade 1978 to 1987, 19 countries reported 10 537 cases. Ten of the countries and 41.9% of the reported cases were in Africa. At least 14.5% of the cases reported in Africa died. Similarly, during the decade 1988 to 1997, 22 countries, 12 of which were in Africa, reported a total of 17,674 cases and 1,465 deaths. Of these, 11,711 cases of which 9.6% died, were reported from Africa.

Africa, Eastern↗
PubMed1991

Imported Plasmodium falciparum malaria in American travelers to Africa. Implications for prevention strategies.

Data from the US National Malaria Surveillance System were analyzed to assess characteristics of travelers who acquired Plasmodium falciparum infections in Africa and evaluate the impact of chloroquine resistance on the incidence of imported malaria. Although the number of cases acquired in East Africa has stabilized, the number of imported P falciparum infections acquired in West Africa increased threefold from 1985 to 1988, and the proportion of travelers who reported failure of chloroquine prophylaxis increased from 10% to 48%. Fifty-eight percent of patients who acquired malaria in West Africa had not used chemoprophylaxis. To curb the rising incidence of P falciparum infections in American travelers, the Centers for Disease Control revised malaria prophylaxis recommendations to include the use of mefloquine in areas of chloroquine resistance. Use of malaria protection measures by travelers to West Africa must also be improved.

Africa, Eastern↗
PubMed1989

Migrant labor and sexually transmitted disease: AIDS in Africa.

Acquired immune deficiency syndrome (AIDS) is worldwide, but the clinical and epidemiological pattern of the disease in Africa is different from that in developed areas. "Type 1 AIDS" occurs in industrialized North America and Europe; it has a distinctive sex ratio (16:1) and risk pattern of IV drug use and sexual practices. "Type 2 AIDS" occurs in Third World countries, particularly in eastern, southern, and central Africa. It is characterized by an entirely different sex ratio (1:1) and by distinctively different risk patterns. Both epidemics are caused by the HIV-1 virus. The key concept for understanding the origins of the differences between Type 1 and Type 2 AIDS is the migratory labor system in eastern, central, and southern Africa. This system causes long absences, increased family breakdown, and increased numbers of sexual partners. Historically the organization of this labor market has created a population which suffers from epidemics of sexually transmitted diseases. These historical patterns are presented as evidence for the contemporary transmission of AIDS. When contemporary AIDS and HIV-1 seropositivity prevalence data are examined, a systematic temporal and geographic pattern emerges for the AIDS epidemic in Africa. Despite a paucity of good data, the prevalence data from eastern, central, and southern Africa support the thesis of migrant labor's role in the transmission of AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed1997

Increasing HIV prevalence in a rural district of South Africa from 1992 through 1995.

OBJECTIVES: To describe the increasing prevalence of HIV infection in a rural district in South Africa, to compare this with a nearby urban setting, and to estimate the prevalence of infection in the general population of the rural district. DESIGN: Serial anonymous cross-sectional HIV seroprevalence surveys among consecutive women attending antenatal clinics in the rural Hlabisa health district, and the urban King Edward VIII Hospital, Durban, South Africa. RESULTS: Crude antenatal HIV seroprevalence in Hlabisa increased from 4.2% (95% confidence interval [95%CI], 3.0-5.7) in 1992, to 14% (95%CI, 10.4-18.4) in 1995 (p < 0.0001). Age-specific prevalence was highest in women aged 20 to 24 years (21.1% in 1995) and in the more urbanized areas of the district (29.5% in 1995). Prevalence in Durban, at 19% (95%CI, 16.5-21.7), was higher than in Hlabisa in 1995 (p = 0.046), in large part as a result of the higher prevalence in the 15 to 19 year age group in Durban (22.4% vs. 7.4%, p = 0.004). An estimated 5.6% (95%CI, 3.0-9.6) of the general population of the Hlabisa district was HIV infected in 1995. CONCLUSIONS: The HIV epidemic, fueled by a high incidence in young people, has escalated rapidly in this part of rural South Africa. Lower crude rural than urban prevalence is largely a result of a lower prevalence in young rural women; the underlying social reasons for this need to be fully explored. South Africa urgently needs to implement effective prevention programs, to plan for the impact of HIV-related disease on the health service, and to develop community-based care strategies.

Adolescent↗
PubMed1996

Sexually transmitted diseases in South Africa.

AIM: To review the epidemiology of and data collection for sexually transmitted diseases (STDs) in South Africa. METHODS: Literature published since 1980 on STDs in South Africa were complied and evaluated. Historical reports and salient unpublished literature were also used in the literature review. Studies were critically reviewed in the light of sample populations and study methods, and a baseline picture of the patterns of STD burden was developed. RESULTS: The STD burden in apparently asymptomatic study populations is significant. Ulcerative infections, primarily caused by syphilis and chancroid, are present in 5-15% of asymptomatic clinic attenders; prevalence rates of gonorrhoea average 8%, with up to 13% of gonococcal isolates resistant to penicillin antibiotics. In addition, on average, chlamydia and vaginal infections are detected in 16% and 20-49%, respectively, of antenatal and family planning clinic attenders. HIV seroprevalence rates have reached 7.6% in antenatal clinic attenders. Most South African STD data are derived from ad hoc surveys which have traditionally focused only on several major infections and particular urban centres. Almost all STD studies have been facility-based, with many studies based at STD clinics, thus reporting only relative frequencies and not population-based prevalences of STDs. With the possible exception of HIV, systematic surveillance data for STDs are conspicuously lacking. CONCLUSION: The disease burden of classic sexually transmitted infections has historically been heavy, and continues to be a serious public health problem in South Africa. Morbidity from both ulcerative and non-ulcerative infections, particularly in women, is significant. The body of STD data, although mostly sound, remains incomplete, and with the rapid emergence of HIV in South Africa, surveillance of STDs and focused STD policies will be critical.

Chancroid↗
PubMed1994

HIV-associated lymphoma in Africa: an autopsy study in Cote d'Ivoire.

HIV infection predisposes to the development of non-Hodgkin lymphoma (NHL). The frequency of NHL among HIV-positive adults and children in sub-Saharan Africa is not known. In 1991-1992, a representative autopsy study of HIV infection was performed in Abidjan, Côte d'Ivoire. Of 247 HIV-positive adult (> 14 years) medical patients dying in hospital, 2.8% had NHL, 1.6% with visceral NHL and 1.2% with primary cerebral lymphoma. The estimated crude incidence of NHL among HIV-positive adults in Abidjan was 84/100,000 per year, 10-fold greater than the expected pre-AIDS incidence of NHL but less than the incidence observed among HIV-positive adults in industrialised countries. None of 78 autopsied HIV-positive children (median age = 17 months) had NHL. HIV infection augments the incidence of NHL among adults in Africa, but short survival with advanced HIV disease probably prevents the major increase in HIV-associated NHL seen in industrialised countries. Survival of HIV-positive children in Africa appears too short to permit the significant development of additional NHL; classic Burkitt lymphoma is not an AIDS-associated tumour in Africa.

Adolescent↗
PubMed1997

Molecular characterisation of type 1 polioviruses associated with epidemics in South Africa.

The molecular epidemiology of wild-type 1 polioviruses isolated in South Africa during 2 major poliomyelitis epidemics in the 1980s and during the pre- and inter-epidemic periods was investigated by partial sequence analysis across the VP1/2A junction. Poliovirus-specific primers were used to amplify and subsequently sequence the region of interest. Viruses belonging to different genotypes were found to have been responsible for the 2 outbreaks. The Gazankulu outbreak in 1982 was caused by a poliovirus genotype which was unique to South Africa and which circulated endemically throughout much of the country between 1980 and 1985. Two additional genotypes, imported from the Middle East and West Africa, cocirculated endemically with the South African genotype between 1982 and 1985. The 1988 epidemic in Kwazulu-Natal was attributed to an imported genotype apparently introduced into South Africa in 1985 from countries north of the border. This genotype displaced the 3 genotypes previously in circulation and continued to be transmitted within the country until 1989, when the last confirmed cases of poliomyelitis associated with wild-type viruses were documented. All circulating wild-type poliovirus strains appear to have been eliminated from South Africa.

Disease Outbreaks↗
PubMed2002

Revised age estimates of Australopithecus-bearing deposits at Sterkfontein, South Africa.

The Sterkfontein fossil site in South Africa has produced the largest concentration of early hominin fossils from a single locality. Recent reports suggest that Australopithecus from this site is found within a broad paleontological age of between 2.5-3.5 Ma (Partridge [2000] The Cenozoic of Southern Africa, Oxford: Oxford Monographs, p. 100-125; Partridge et al. [2000a], The Cenozoic of Southern Africa, Oxford: Oxford Monographs, p. 129-130; Kuman and Clarke [2000] J Hum Evol 38:827-847). Specifically, the hominin fossil commonly referred to as the "Little Foot" skeleton from Member 2, which is arguably the most complete early hominin skeleton yet discovered, has been magnetostratigraphically dated to 3.30-3.33 Ma (Partridge [2000] The Cenozoic of Southern Africa, Oxford: Oxford Monographs, p. 100-125; Partridge et al. [2000a], The Cenozoic of Southern Africa, Oxford: Oxford Monographs, p. 129-130). More recent claims suggest that hominin fossils from the Jacovec Cavern are even older, being dated to approximately 3.5 Ma. Our interpretation of the fauna, the archeometric results, and the magnetostratigraphy of Sterkfontein indicate that it is unlikely that any Members yet described from Sterkfontein are in excess of 3.04 Ma in age. We estimate that Member 2, including the Little Foot skeleton, is younger than 3.0 Ma, and that Member 4, previously dated to between 2.4-2.8 Ma, is more likely to fall between 1.5-2.5 Ma. Our results suggest that Australopithecus africanus should not be considered as a temporal contemporary of Australopithecus afarensis, Australopithecus bahrelghazali, and Kenyanthropus platyops.

Animals↗
PubMed2002

Backed tools in Middle Pleistocene central Africa and their evolutionary significance.

The fashioning of stone inserts for composite tools by blunting flakes and blades is a technique usually associated with Late Pleistocene modern humans. Recent reports from two sites in south central Africa (Twin Rivers and Kalambo Falls) suggest that this backed tool technology originated in the later Middle Pleistocene with early or "archaic" Homo sapiens. This paper investigates these claims critically from the perspective of the potential mixing of Middle and Later Stone Age deposits at the two sites and the possible creation of misleading assemblages. The review shows that backed tools form a statistically minor, but technologically significant feature of the early Middle Stone Age of south central Africa. They first appear in the Lupemban industry at approximately 300 ka and remain an element of the Middle Stone Age technological repertoire of the region. Comparisons are made with early backed tool assemblages of east Africa and with the much younger Howiesons Poort industry of southern Africa. The paper concludes that Lupemban tools lack the standardization of the Howiesons Poort backed pieces, but form part of a regionally distinctive and diverse assemblage of heavy and light duty tools. Some modern-like behaviours appear to have emerged by the later Middle Pleistocene in south central Africa.

Africa↗
PubMed2000

Molecular variability of geographically distinct isolates of Rice yellow mottle virus in Africa.

The coat protein gene (ORF4) and the 3' untranslated region of a sample of 40 isolates of Rice yellow mottle virus (RYMV), 32 from West Africa and 8 from East Africa, have been sequenced. Five major strains were differentiated, three from West Africa (S1, S2, S3) and two from East Africa (S4, S5), with a spatial overlap of the strains within each of these two regions. Nucleotide and amino-acid divergence between strains was up to 11%. Although more isolates from West African were sequenced, variability was twofold lower than among East African isolates. Variability in ORF4 and in ORF2 coincided. Within strain and within isolate variations in nucleotide sequences were low. Bipartite nuclear targeting motif, Ca2+ binding sites and at least two stretches of amino-acids were conserved among the 40 RYMV isolates and the other sobemoviruses. Variants associating sequence motifs characteristic of different strains have been found, possibly resulting from recombination events. Differences in pathogenicity among isolates were associated with changes of amino-acids in the bipartite nuclear targeting motif of the R domain of the capsid protein, and around conserved positions 151-154 of the S domain. We hypothesise that the observed pattern of variation of RYMV reflects the effect of spatial isolation between East and West Africa coupled with adaptive changes associated to the original virus reservoirs of the different strains.

3' Untranslated Regions↗