Determinants of the haemoglobin level in patients with sickle cell disease living in sub-Saharan Africa: Major impact of the country of residence and independent effects of leucocyte and platelet counts and haemolysis.

The degree of anaemia in sickle cell disease (SCD) is a well-known contributor to morbidity and mortality. We aimed to explore the factors affecting haemoglobin (Hb) level in African SCD patients, considering haemolysis biomarkers (LDH and bilirubin level, and reticulocyte count), leucocyte and platelet counts and socio-demographic characteristics (gender, age group, country of residence and BMI). The research was part of the CADRE multinational cohort and involved 3699 SCD patients living in Mali, Senegal, Ivory Coast, Democratic Republic of Congo, Gabon and Cameroon: 2936 SS/Sß0, 587 SC and 176 Sß + patients with median Hb level of 8, 11.3 and 11.2 g/dL respectively (p < 0.001). In multivariate analysis conducted in 1394 SS/Sß0 patients, living in Cameroon, female gender, lower BMI, higher haemolysis markers (especially LDH) and higher leucocyte and platelet counts were independently associated with lower Hb level (all p < 0.05). In 497 SC and 156 Sß + patients, female gender (p < 0.001), lower BMI (p < 0.05) and higher platelet counts (p < 0.001) were independently associated with lower Hb level. Anaemia in African SCD patients is not only associated with haemolysis but also with the country of residence, lower BMI and leucocyte or platelet counts which might reflect inflammation related to infectious burden in the region.

ICTV Virus Taxonomy Profile: Arenaviridae 2023.

Arenaviridae is a family for ambisense RNA viruses with genomes of about 10.5 kb that infect mammals, snakes, and fish. The arenavirid genome consists of two or three single-stranded RNA segments and encodes a nucleoprotein (NP), a glycoprotein (GP) and a large (L) protein containing RNA-directed RNA polymerase (RdRP) domains; some arenavirids encode a zinc-binding protein (Z). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Arenaviridae, which is available at www.ictv.global/report/arenaviridae.

Serological evidence of Rift Valley fever virus infection among domestic ruminant herds in Uganda.

BACKGROUND: Prior to the first recorded outbreak of Rift Valley fever (RVF) in Uganda, in March 2016, earlier studies done until the 1970's indicated the presence of the RVF virus (RVFV) in the country, without any recorded outbreaks in either man or animals. While severe outbreaks of RVF occurred in the neighboring countries, none were reported in Uganda despite forecasts that placed some parts of Uganda at similar risk. The Ministry of Agriculture, Animal Industry and Fisheries (MAAIF) undertook studies to determine the RVF sero-prevalence in risk prone areas. Three datasets from cattle sheep and goats were obtained; one from retrospective samples collected in 2010-2011 from the northern region; the second from the western region in 2013 while the third was from a cross-sectional survey done in 2016 in the south-western region. Laboratory analysis involved the use of the Enzyme Linked Immunosorbent Assays (ELISA). Data were subjected to descriptive statistical analyses, including non-parametric chi-square tests for comparisons between districts and species in the regions. RESULTS: During the Yellow Fever outbreak investigation of 2010-2011 in the northern region, a total sero-prevalence of 6.7% was obtained for anti RVFV reacting antibodies (IgG and IgM) among the domestic ruminant population. The 2013 sero-survey in the western region showed a prevalence of 18.6% in cattle and 2.3% in small ruminants. The 2016 sero-survey in the districts of Kabale, Kanungu, Kasese, Kisoro and Rubirizi, in the south-western region, had the respective district RVF sero-prevalence of 16.0, 2.1, 0.8, 15.1and 2.7% among the domestic ruminants combined for this region; bovines exhibited the highest cumulative sero-prevalence of 15.2%, compared to 5.3 and 4.0% respectively for sheep and goats per species for the region. CONCLUSIONS: The absence of apparent outbreaks in Uganda, despite neighboring enzootic areas, having minimal restrictions to the exchange of livestock and their products across borders, suggest an unexpected RVF activity in the study areas that needs to be unraveled. Therefore, more in-depth studies are planned to mitigate the risk of an overt RVF outbreak in humans and animals as has occurred in neighboring countries.

Rabies in Uganda: rabies knowledge, attitude and practice and molecular characterization of circulating virus strains.

BACKGROUND: Rabies is a deadly preventable viral disease that affects all warm-blooded animals and widespread in many regions including Africa. The disease remains of major public health importance in Uganda. The purpose of this study was to establish Knowledge, Attitude, Practice (KAP) of Rabies in Moyo and Ntoroko districts and to characterize Rabies virus (RABV) strains from seven districts of Uganda with consistent prevalence of rabies. METHODS: KAP survey data were collected based on animal biting history by interviewing the head of the veterinary departments, the medical centers and selected households from the study sites. Data were obtained from 84 households in Ntoroko and Moyo districts. Thirty-five (35) brain samples were collected from bovine, dogs, goats, foxes, jackals ad sheep between 2011 and 2013. Samples were tested using fluorescent antibody test (FAT), One step RT-PCR (following RNA extraction) and partial RABV N gene was sequenced by Sanger method before phylogenetic and phylogeographic analyses of sequences. RESULTS: Scarcity of post-exposure prophylaxis services in the health centers was noted. Poor attitude of wound washing and deficiency of knowledge on how to handle wounds related to dog bites and the significance among household participants lacked. There is a high risk of rabies infection due to a limited dog's vaccination. Dog biting episodes in humans were of 75.00 and 62.50% in Moyo and Ntoroko districts respectively. Twenty-seven (27) samples tested positive for rabies by FAT and PCR. Ugandan sequences were closely related (97% nucleotide id) to the rabies virus sequences from Tanzania, Rwanda, Burundi, Nigeria, Central African Republic and Sudan with both the "Africa 1A" and "Africa 1B" RABV clades represented. A putative new clade 1D was also detected. CONCLUSIONS: Rabies remains a public health hazard in Uganda. There is urgent need to establish advocacy programs in both schools and communities to curtail the spread of rabies. Increasing the knowledge regarding wound washing, post-exposure prophylaxis and dogs vaccination would enhance prevention of rabies. A strong collaboration between medical and veterinary sectors under a one health platform is required to ensure sufficient preventative services to the communities.

Human Monkeypox in Sierra Leone after 44-Year Absence of Reported Cases.

We note the reemergence of human monkeypox in Sierra Leone following a 44-year absence of reported disease. The persons affected were an 11-month-old boy and, several years later, a 35-year-old man. The reappearance of monkeypox in this country suggests a need for renewed vigilance and awareness of the disease and its manifestations.

ICTV Virus Taxonomy Profile: Arenaviridae.

Members of the family Arenaviridae produce enveloped virions containing genomes consisting of two or three single-stranded RNA segments totalling about 10.5 kb. Arenaviruses can infect mammals, including humans and other primates, snakes, and fish. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Arenaviridae, which is available at www.ictv.global/report/arenaviridae.

Taxonomy of the order Bunyavirales: update 2019.

In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Taxonomy of the order Bunyavirales: second update 2018.

In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

The score of integrated disease surveillance and response adequacy (SIA): a pragmatic score for comparing weekly reported diseases based on a systematic review.

BACKGROUND: The Integrated Disease Surveillance and Response (IDSR) strategy implemented by the World Health Organization (WHO) in Africa has produced a large amount of data on participating countries, and in particular on the Democratic Republic of Congo (DRC). These data are increasingly considered as unevaluable and, therefore, as requiring a rigorous process of validation before they can be used for research or public health purposes. The aim of this study was to propose a method to assess the level of adequacy of IDSR morbidity data in reflecting actual morbidity. METHODS: A systematic search of English- and French-language articles was performed in Scopus, Medline, Science Direct, Springer Link, Cochrane, Cairn, Persée, and Erudit databases. Other types of documents were identified through manual searches. Selected articles focused on the determinants of the discrepancies (differences) between reported morbidity and actual morbidity. An adequacy score was constructed using some of the identified determinants. This score was applied to the 15 weekly reported diseases monitored by IDSR surveillance in the DRC. A classification was established using the Jenks method and a sensitivity analysis was performed. Twenty-three classes of determinants were identified in 35 IDSR technical guides and reports of outbreak investigations and in 71 out of 2254 researched articles. For each of the 15 weekly reported diseases, the SIA was composed of 12 items grouped in 6 dimensions. RESULTS: The SIA classified the 15 weekly reported diseases into 3 categories or types: high score or good adequacy (value > = 14), moderate score or fair adequacy (value > = 8 and < 14), and low score or low or non-adequacy (value < 8). Regardless of the criteria used in the sensitivity analysis, there was no notable variation in SIA values or categories for any of the 15 weekly reported diseases. CONCLUSION: In a context of sparse health information in low- and middle-income countries, this study developed a score to help classify IDSR morbidity data as usable, usable after adjustment, or unusable. This score can serve to prioritize, optimize, and interpret data analyses for epidemiological research or public health purposes.

Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.

Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment. [Arenaviridae; binomials; ICTV; International Committee on Taxonomy of Viruses; Mononegavirales; virus nomenclature; virus taxonomy.].

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Rift Valley fever seroprevalence and abortion frequency among livestock of Kisoro district, South Western Uganda (2016): a prerequisite for zoonotic infection.

BACKGROUND: Rift Valley fever (RVF) is classified as viral hemorrhagic fever and is endemic in East and West Africa. RVF is caused by an arthropod borne virus (RVFV); the disease is zoonotic and affects human, animal health as well as international trade. In livestock it causes abortions, while human infection occurs through close contact with infected animals or animal products. METHODS: A quantitative observational study using stratified sampling was conducted in the western region of Uganda. Blood samples and abortion events from 1000 livestock (goats, sheep and cattle) was collected and recorded. Serum was analyzed for RVFV IgG reacting antibodies using competitive ELISA test. RESULTS: The overall RVFV seroprevalence was of 10.4% (104/1000). Cattle had the highest seroprevalence (7%) followed by Sheep (2.2%) then goats (1.2%). Species specific RVFV seroprevalence was highest in cattle (20.5%) followed by sheep (6.8%) then goats (3.6%). RVFV seroprevalence in northern highlands (21.8%) was significantly higher (p < 0.001) than in the southern lowlands (3.7%). Overall prevalence of abortion was (17.4%), sheep had the highest prevalence of abortion (7.8%) followed by goats (6.3%) and then cattle (3.3%). Species specific abortion prevalence was highest in Sheep (24.1%) followed by goats (18.8%) and then 9.7% in cattle. CONCLUSION: RVFV is endemic in Kisoro district and livestock in the highland areas are more likely to be exposed to RVFV infection compared to those in the southern lowlands. Out breaks in livestock most likely will lead to zoonotic infection in Kisoro district.

Assessing short evolution brucellosis in a highly brucella endemic cattle keeping population of Western Uganda: a complementary use of Rose Bengal test and IgM rapid diagnostic test.

BACKGROUND: Brucellosis is a worldwide and zoonotic disease often sadly misdiagnosed in endemic areas. Challenges of availability and accessibility of diagnostic tools are common in resource constrained populations where the most vulnerable are found, surveillance and diagnosis are limited too. METHODS: A cross-sectional study using a simple two stage cluster sampling method was conducted to measure short evolution brucellosis burden among cattle keeping households that are one of the highest risk populations to be exposed to Brucella infection. A total of 216 households were randomly selected from 18 rural villages from the Western Region of Uganda. Household blood samples were tested for Brucella antibodies using the highly sensitive Rose Bengal test (RBT) and IgM ELISA Lateral Flow Assay (LFA). RESULTS: Among the total tested population, 58.8% did not react with any of the tests, 13.4% reacted with both tests. Among those that reacted with both (N = 29), 62.1% had weak (+ 1) LFA staining, 34.5% had moderate (2+) LFA staining. Altogether, both weak and moderate staining (96.5%) are consistent with sub-acute disease, while only one (3.4%) had strong (3+) LFA staining consistent with acute infection. 19.4% of the samples tested positive only with RBT, consistent with chronic infection, eighteen samples (8.3%) reacted exclusively with IgM LFA. CONCLUSION: We identified a high prevalence of short evolution brucellosis in the cattle keeping household members. Prevalence of chronic infection diagnosed with RBT only was higher than the prevalence of short evolution brucellosis. IgM LFA results depict possible cases of cross reaction with Salmonella spp., Plasmodium etc. Ultimately, we identified a consistent prevalence of short evolution brucellosis in the cattle keeping household members. Indeed, the use of a combined diagnostic with LFA and RBT is easy and amenable for an active disease surveillance and accurate diagnosis in rural settings.

Malaria continues to select for sickle cell trait in Central Africa.

Sickle cell disease (SCD) is a genetic disorder that poses a serious health threat in tropical Africa, which the World Health Organization has declared a public health priority. Its persistence in human populations has been attributed to the resistance it provides to Plasmodium falciparum malaria in its heterozygous state, called sickle cell trait (SCT). Because of migration, SCT is becoming common outside tropical countries: It is now the most important genetic disorder in France, affecting one birth for every 2,400, and one of the most common in the United States. We assess the strength of the association between SCT and malaria, using current data for both SCT and malaria infections. A total of 3,959 blood samples from 195 villages distributed over the entire Republic of Gabon were analyzed. Hemoglobin variants were identified by using HPLCy (HPLC). Infections by three species of Plasmodium were detected by PCR followed by sequencing of a 201-bp fragment of cytochrome b. An increase of 10% in P. falciparum malaria prevalence is associated with an increase by 4.3% of SCT carriers. An increase of 10 y of age is associated with an increase by 5.5% of SCT carriers. Sex is not associated with SCT. These strong associations show that malaria remains a selective factor in current human populations, despite the progress of medicine and the actions undertaken to fight this disease. Our results provide evidence that evolution is still present in humans, although this is sometimes questioned by scientific, political, or religious personalities.

Arterial Stiffness Impairment in Sickle Cell Disease Associated With Chronic Vascular Complications: The Multinational African CADRE Study.

BACKGROUND: Although a blood genetic disease, sickle cell disease (SCD) leads to a chronic vasculopathy with multiple organ involvement. We assessed arterial stiffness in SCD patients and looked for associations between arterial stiffness and SCD-related vascular complications. METHODS: The CADRE (Coeur Artères et Drepanocytose, ie, Heart Arteries and Sickle Cell Disease) study prospectively recruited pediatric and adult SCD patients and healthy controls in Cameroon, Ivory Coast, Gabon, Mali, and Senegal. Patients underwent clinical examination, routine laboratory tests (complete blood count, serum creatinine level), urine albumin/creatinine ratio measure, and a measure of carotid-femoral pulse wave velocity (cf-PWV) and augmentation index (AI) at a steady state. The clinical and biological correlates of cf-PWV and AI were investigated by using a multivariable multilevel linear regression analysis with individuals nested in families further nested in countries. RESULTS: Included were 3627 patients with SCD and 943 controls. Mean cf-PWV was lower in SCD patients (7.5±2.0 m/s) than in controls (9.1±2.4 m/s, P<0.0001), and lower in SS-Sß(0) than in SC-Sß(+) phenotypes. AI, corrected for heart rate, increased more rapidly with age in SCD patients and was higher in SCD than in control adults. cf-PWV and AI were independently associated with age, sex, height, heart rate, mean blood pressure, hemoglobin level, country, and hemoglobin phenotype. After adjustment for these correlates, cf-PWV and AI were associated with the glomerular filtration rate and osteonecrosis. AI was also associated with stroke, pulmonary hypertension, and priapism, and cf-PWV was associated with microalbuminuria. CONCLUSIONS: PWV and AI are deeply modified in SCD patients in comparison with healthy controls. These changes are independently associated with a lower blood pressure and a higher heart rate but also with the hemoglobin phenotype. Moreover, PWV and AI are associated with several SCD clinical complications. Their prognostic value will be assessed at follow-up of the patients.

Differentiation of Staphylococcus argenteus (formerly: Staphylococcus aureus clonal complex 75) by mass spectrometry from S. aureus using the first strain isolated from a wild African great ape.

The species Staphylococcus argenteus was separated recently from Staphylococcus aureus (Tong S.Y., F. Schaumburg, M.J. Ellington, J. Corander, B. Pichon, F. Leendertz, S.D. Bentley, J. Parkhill, D.C. Holt, G. Peters, and P.M. Giffard, 2015). The objective of this work was to characterise the genome of a non-human S. argenteus strain, which had been isolated from the faeces of a wild-living western lowland gorilla in Gabon, and analyse the spectrum of this species in matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The full genome sequence revealed a scarcity of virulence genes and absence of resistance genes, indicating a decreased virulence potential compared to S. aureus and the human methicillin-resistant S. argenteus isolate MSHR1132T. Spectra obtained by MALDI-TOF MS and the analysis of available sequences in the genome databases identified several MALDI-TOF MS signals that clearly differentiate S. argenteus, the closely related Staphylococcus schweitzeri and S. aureus. In conclusion, in the absence of biochemical tests that identify the three species, mass spectrometry should be employed as method of choice.

An assessment of caprine tuberculosis prevalence in Lubumbashi slaughterhouse, Democratic Republic of Congo.

Caprine tuberculosis is a major health problem for goats and a major zoonosis of veterinary public health interest. In order to prepare a response to and control of caprine tuberculosis, to evaluate the potential risks to public health, and to assess the prevalence of the disease in Katanga province, Democratic Republic of Congo, 656 goats that were slaughtered at the Kabasele abattoir of Mzee Laurent-Desire Kabila Market in Lubumbashi were subjected to rigorous veterinary inspection during June to August 2012. All goat specimens came from the Kasumbalesa, Kasenga, and Kipushi areas of Katanga province. Consequently, suspected organs presenting signs of tuberculosis were collected and examined using Ziehl-Neelsen stains for diagnosis. Through this investigative inspection in the province, we found an overall prevalence of caprine tuberculosis of 1.68%. Although females showed higher prevalence of caprine tuberculosis (1.07%) compared to males (0.61%), and adults showed higher prevalence (1.22%) than juveniles (0.45%), these comparisons were not statically significant. However, lung and intestine infection by tuberculosis showed significantly higher prevalence of positive cases (1.21 and 0.46%, respectively) (p < 0.05). Goats from Kasumbalesa had the highest prevalence of caprine tuberculosis (1.22%) compared to goats from Kipushi (0.31%) and Kasenga (0.18%). These findings show the risk of caprine tuberculosis in the province for the first time, and we therefore recommend the implementation of strict animal biosecurity and tuberculosis controlling protocols.

Serosurveillance of viral pathogens circulating in West Africa.

BACKGROUND: Sub-Saharan Africa is home to a variety of pathogens, but disease surveillance and the healthcare infrastructure necessary for proper management and control are severely limited. Lassa virus, the cause of Lassa fever, a severe hemorrhagic fever in humans is endemic in West Africa. In Sierra Leone at the Kenema Government Hospital Lassa Diagnostic Laboratory, up to 70 % of acute patient samples suspected of Lassa fever test negative for Lassa virus infection. This large amount of acute undiagnosed febrile illness can be attributed in part to an array of hemorrhagic fever and arthropod-borne viruses causing disease that goes undetected and untreated. METHODS: To better define the nature and extent of viral pathogens infecting the Sierra Leonean population, we developed a multiplexed MAGPIX® assay to detect IgG antibodies against Lassa, Ebola, Marburg, Rift Valley fever, and Crimean-Congo hemorrhagic fever viruses as well as pan-assays for flaviviruses and alphaviruses. This assay was used to survey 675 human serum samples submitted to the Lassa Diagnostic Laboratory between 2007 and 2014. RESULTS: In the study population, 50.2 % were positive for Lassa virus, 5.2 % for Ebola virus, 10.7 % for Marburg virus, 1.8 % for Rift Valley fever virus, 2.0 % for Crimean-Congo hemorrhagic fever virus, 52.9 % for flaviviruses and 55.8 % for alphaviruses. CONCLUSIONS: These data exemplify the importance of disease surveillance and differential diagnosis for viral diseases in Sierra Leone. We demonstrate the endemic nature of some of these viral pathogens in the region and suggest that unrecognized outbreaks of viral infection have occurred.

Past, present, and future of arenavirus taxonomy.

Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The paradigm of arenaviruses exclusively infecting small mammals shifted dramatically when several groups independently published the detection and isolation of a divergent group of arenaviruses in captive alethinophidian snakes. Preliminary phylogenetic analyses suggest that these reptilian arenaviruses constitute a sister clade to mammalian arenaviruses. Here, the members of the International Committee on Taxonomy of Viruses (ICTV) Arenaviridae Study Group, together with other experts, outline the taxonomic reorganization of the family Arenaviridae to accommodate reptilian arenaviruses and other recently discovered mammalian arenaviruses and to improve compliance with the Rules of the International Code of Virus Classification and Nomenclature (ICVCN). PAirwise Sequence Comparison (PASC) of arenavirus genomes and NP amino acid pairwise distances support the modification of the present classification. As a result, the current genus Arenavirus is replaced by two genera, Mammarenavirus and Reptarenavirus, which are established to accommodate mammalian and reptilian arenaviruses, respectively, in the same family. The current species landscape among mammalian arenaviruses is upheld, with two new species added for Lunk and Merino Walk viruses and minor corrections to the spelling of some names. The published snake arenaviruses are distributed among three new separate reptarenavirus species. Finally, a non-Latinized binomial species name scheme is adopted for all arenavirus species. In addition, the current virus abbreviations have been evaluated, and some changes are introduced to unequivocally identify each virus in electronic databases, manuscripts, and oral proceedings.

Men, primates, and germs: an ongoing affair.

Humans and nonhuman primates are phylogenetically (i.e., genetically) related and share pathogens that can jump from one species to another. The specific strategies of three groups of pathogens for crossing the species barrier among primates will be discussed. In Africa, gorillas and chimpanzees have succumbed for years to simultaneous epizootics (i.e.. "multi-emergence") of Ebola virus in places where they are in contact with Chiropters, which could be animal reservoirs of these viruses. Human epidemics often follow these major outbreaks. Simian immunodeficiency viruses (SIVs) have an ancient history of coevolution and many interspecific exchanges with their natural hosts. Chimpanzee and gorilla SIVs have crossed the species barrier at different times and places, leading to the emergence of HIV-1 and HIV-2. Other retroviruses, such as the Simian T-Lymphotropic Viruses and Foamiviruses, have also a unique ancient or recent history of crossing the species barrier. The identification of gorilla Plasmodium parasites that are genetically close to P. falciparum suggests that gorillas were the source of the deadly human P. falciparum. Nonhuman plasmodium species that can infect humans represent an underestimated risk.