Distribution and diversity of local strains of rice yellow motile virus in Tanzania

Rice (Oryza sativa) is a key staple in Tanzania but its productivity is affected by disease infestation, primary among which is the rice yellow mottle virus (RYMV). Tanzania possesses high RYMV densities and several locations including the Eastern Arc Mountains provide suitable habitat fragmentation that facilitates the diversification process of the virus. However, the distribution pattern and diversity of the local strains of RYMV remain largely unknown and this hinders progress in designing interventions. Efforts were, therefore, made to study the pattern and distribution of RYMV. Collection of isolates was made in May; recovery of virus on a susceptible elite line viz. TXD 220-1-3-3-1 was in June-July and molecular analysis was done in September-December 2005. The sequences of the coat protein (CP) gene of 23 isolates, representative of the three strains of RYMV found in Tanzania, were selected from 52 isolates collected from three regions. The phylogenetic analyses of the CP sequences revealed high (14.8%) nucleotide divergence between strains. Strain S6 was the most divergent with an intra- strain nucleotide divergence of 8.8%; this was consistent with its wide distribution in the region and particularly the eastern part of the Tanzania. Isolates of strains S4 were recorded for the first time in the eastern Arc Mountain region. These formed a monophyletic group with the Lake Malawi strain S4 sub-lineage (percentage identity of 95.4 to 96.8%) and differed from the Lake Victoria strain S4 sub-lineage by 4.5%. Coexistence within the same field of S4, S5 and S6 isolates was observed in the eastern Arc Mountains region. Strong competition between strains of RYMV was suspected from the limited distribution and rarity of strain S5. This study confirm speculations that the Eastern Arc Mountain region is the centre of origin of RYMV. Thus, the high viral load in the Eastern Arc Mountain imply that it is a suitable location for strategic studies aimed at designing control interventions against RYMV

Predictive value of clinical and laboratory features for the main febrile diseases in children living in Tanzania: A prospective observational study.

To construct evidence-based guidelines for management of febrile illness, it is essential to identify clinical predictors for the main causes of fever, either to diagnose the disease when no laboratory test is available or to better target testing when a test is available. The objective was to investigate clinical predictors of several diseases in a cohort of febrile children attending outpatient clinics in Tanzania, whose diagnoses have been established after extensive clinical and laboratory workup. From April to December 2008, 1005 consecutive children aged 2 months to 10 years with temperature ≥38°C attending two outpatient clinics in Dar es Salaam were included. Demographic characteristics, symptoms and signs, comorbidities, full blood count and liver enzyme level were investigated by bi- and multi-variate analyses (Chan, et al., 2008). To evaluate accuracy of combined predictors to construct algorithms, classification and regression tree (CART) analyses were also performed. 62 variables were studied. Between 4 and 15 significant predictors to rule in (aLR+>1) or rule out (aLR+<1) the disease were found in the multivariate analysis for the 7 more frequent outcomes. For malaria, the strongest predictor was temperature ≥40°C (aLR+8.4, 95%CI 4.7-15), for typhoid abdominal tenderness (5.9,2.5-11), for urinary tract infection (UTI) age ≥3 years (0.20,0-0.50), for radiological pneumonia abnormal chest auscultation (4.3,2.8-6.1), for acute HHV6 infection dehydration (0.18,0-0.75), for bacterial disease (any type) chest indrawing (19,8.2-60) and for viral disease (any type) jaundice (0.28,0.16-0.41). Other clinically relevant and easy to assess predictors were also found: malaria could be ruled in by recent travel, typhoid by jaundice, radiological pneumonia by very fast breathing and UTI by fever duration of ≥4 days. The CART model for malaria included temperature, travel, jaundice and hepatomegaly (sensitivity 80%, specificity 64%); typhoid: age ≥2 years, jaundice, abdominal tenderness and adenopathy (46%,93%); UTI: age <2 years, temperature ≥40°C, low weight and pale nails (20%,96%); radiological pneumonia: very fast breathing, chest indrawing and leukocytosis (38%,97%); acute HHV6 infection: less than 2 years old, (no) dehydration, (no) jaundice and (no) rash (86%,51%); bacterial disease: chest indrawing, chronic condition, temperature ≥39.7°c and fever duration >3 days (45%,83%); viral disease: runny nose, cough and age <2 years (68%,76%). A better understanding of the relative performance of these predictors might be of great help for clinicians to be able to better decide when to test, treat, refer or simply observe a sick child, in order to decrease morbidity and mortality, but also to avoid unnecessary antimicrobial prescription. These predictors have been used to construct a new algorithm for the management of childhood illnesses called ALMANACH

Beyond malaria--causes of fever in outpatient Tanzanian children.

BACKGROUND: As the incidence of malaria diminishes, a better understanding of nonmalarial fever is important for effective management of illness in children. In this study, we explored the spectrum of causes of fever in African children. METHODS: We recruited children younger than 10 years of age with a temperature of 38°C or higher at two outpatient clinics--one rural and one urban--in Tanzania. Medical histories were obtained and clinical examinations conducted by means of systematic procedures. Blood and nasopharyngeal specimens were collected to perform rapid diagnostic tests, serologic tests, culture, and molecular tests for potential pathogens causing acute fever. Final diagnoses were determined with the use of algorithms and a set of prespecified criteria. RESULTS: Analyses of data derived from clinical presentation and from 25,743 laboratory investigations yielded 1232 diagnoses. Of 1005 children (22.6% of whom had multiple diagnoses), 62.2% had an acute respiratory infection; 5.0% of these infections were radiologically confirmed pneumonia. A systemic bacterial, viral, or parasitic infection other than malaria or typhoid fever was found in 13.3% of children, nasopharyngeal viral infection (without respiratory symptoms or signs) in 11.9%, malaria in 10.5%, gastroenteritis in 10.3%, urinary tract infection in 5.9%, typhoid fever in 3.7%, skin or mucosal infection in 1.5%, and meningitis in 0.2%. The cause of fever was undetermined in 3.2% of the children. A total of 70.5% of the children had viral disease, 22.0% had bacterial disease, and 10.9% had parasitic disease. CONCLUSIONS: These results provide a description of the numerous causes of fever in African children in two representative settings. Evidence of a viral process was found more commonly than evidence of a bacterial or parasitic process. (Funded by the Swiss National Science Foundation and others.)

Single nucleotide variations in CLCN6 identified in patients with benign partial epilepsies in infancy and/or febrile seizures

Nucleotide alterations in the gene encoding proline-rich transmembrane protein 2 (PRRT2) have been identified in most patients with benign partial epilepsies in infancy (BPEI)/benign familial infantile epilepsy (BFIE). However, not all patients harbor these PRRT2 mutations, indicating the involvement of genes other than PRRT2. In this study, we performed whole exome sequencing analysis for a large family affected with PRRT2-unrelated BPEI. We identified a non-synonymous single nucleotide variation (SNV) in the voltage-sensitive chloride channel 6 gene (CLCN6). A cohort study of 48 BPEI patients without PRRT2 mutations revealed a different CLCN6 SNV in a patient, his sibling and his father who had a history of febrile seizures (FS) but not BPEI. Another study of 48 patients with FS identified an additional SNV in CLCN6. Chloride channels (CLCs) are involved in a multitude of physiologic processes and some members of the CLC family have been linked to inherited diseases. However, a phenotypic correlation has not been confirmed for CLCN6. Although we could not detect significant biological effects linked to the identified CLCN6 SNVs, further studies should investigate potential CLCN6 variants that may underlie the genetic susceptibility to convulsive disorders.Toshiyuki Yamamoto, Keiko Shimojima, Noriko Sangu, Yuta Komoike, Atsushi Ishii, Shinpei Abe, Shintaro Yamashita, Katsumi Imai, Tetsuo Kubota, Tatsuya Fukasawa, Tohru Okanishi, Hideo Enoki, Takuya Tanabe, Akira Saito, Toru Furukawa, Toshiaki Shimizu, Carol J. Milligan, Steven Petrou, Sarah E. Heron, Leanne M. Dibbens, Shinichi Hirose, Akihisa Okumur

Dating of the Black Sea Basin: New nannoplankton ages from its inverted margin in the Central Pontides (Turkey)

International audienceThe Eocene uplift and inversion of a part of the Black Sea margin in the Central Pontides, allows to study the stratigraphic sequence of the Western Black Sea Basin. The revision of this sequence, with 164 nannoplankton ages, indicates that subsidence and rifting started in the Upper Barremian and accelerated during the Aptian. The rifting of the Western Black Sea Basin lasted about 40 Myr (from late Barremian to Coniacian). In the inner, inverted, Black Sea margin, the syn-rift sequence ends up with shallow marine sands. The uppermost Albian to Turonian was a period of erosion or non deposition. This regional mid-Cretaceous stratigraphical gap might result from rift flank uplift, as expected in the case of a thick and cold pre-rift lithosphere. However, coeval collision of the Kargi Block, along the North Tethyan subduction zone at the southern margin of the Pontides, might also have contributed to this uplift. A rapid thermal post-rift subsidence of the margin occurred during the Coniacian-Santonian. Collision of the Kirşehir continental block commenced in Early Eocene time (zone NP12) giving rise to compressional deformation and sedimentation in piggyback basins in the Central Pontides, whereas the eastern Black Sea was still opening

Distribution and Diversity of Local Strains of Rice Yellow Mottle Virus in Tanzania

Rice ( Oryza sativa ) is a key staple in Tanzania but its productivity is affected by disease infestation, primary among which is the rice yellow mottle virus (RYMV). Tanzania possesses high RYMV densities and several locations including the Eastern Arc Mountains provide suitable habitat fragmentation that facilitates the diversification process of the virus. However, the distribution pattern and diversity of the local strains of RYMV remain largely unknown and this hinders progress in designing interventions. Efforts were, therefore, made to study the pattern and distribution of RYMV. Collection of isolates was made in May; recovery of virus on a susceptible elite line viz. TXD 220-1-3-3-1 was in June-July and molecular analysis was done in September-December 2005. The sequences of the coat protein (CP) gene of 23 isolates, representative of the three strains of RYMV found in Tanzania, were selected from 52 isolates collected from three regions. The phylogenetic analyses of the CP sequences revealed high (14.8%) nucleotide divergence between strains. Strain S6 was the most divergent with an intra- strain nucleotide divergence of 8.8%; this was consistent with its wide distribution in the region and particularly the eastern part of the Tanzania. Isolates of strains S4 were recorded for the first time in the eastern Arc Mountain region. These formed a monophyletic group with the Lake Malawi strain S4 sub-lineage (percentage identity of 95.4 to 96.8%) and differed from the Lake Victoria strain S4 sub-lineage by 4.5%. Coexistence within the same field of S4, S5 and S6 isolates was observed in the eastern Arc Mountains region. Strong competition between strains of RYMV was suspected from the limited distribution and rarity of strain S5. This study confirm speculations that the Eastern Arc Mountain region is the centre of origin of RYMV. Thus, the high viral load in the Eastern Arc Mountain imply that it is a suitable location for strategic studies aimed at designing control interventions against RYMV.Le riz ( Oryza sativa ) est un aliment de base en Tanzanie, mais sa productivité est significativement entamée par l'infestation des maladies, parmi laquelle est le virus jaune marbre de riz (RYMV). La Tanzanie possède les hautes densités de RYMV et plusieurs endroits y compris les Montagnes d'Arc d'Est fournissent de pochettes d'habitat qui facilite le processus de diversification du virus. Cependant, le modèle de distribution et la diversité des variétés locales de RYMV restent principalement inconnus et ceci freine le progrès dans la conception des interventions. Les efforts étaient, donc faits d'étudier la tendance et la distribution de RYMV. La collection des isolées a été faite au mois de mai ; i.e le rétablissement de virus sur une ligne d'élite susceptible. TXD 220-1-3-31 était fait au mois entre juin et juillet et l'analyse moléculaire a été faite entre septembre et décembre 2005. Les séquences de la protéine de manteau (PC) gênes de 23 isolées, été choisi de 52 isolées collectionnées dans trois régions. L'analyse phylogénétique des séquences de PC a révélé une grande (14.8%) divergence de nucléotides entre les variétés. S6 était la plus divergente avec une intra - divergence de nucléotide de 8,8% ; ceci était conforme à sa large distribution dans la région et notamment la partie Est de la Tanzanie. Les Isolées de S4 ont été identifiées pour la première fois dans la région de Montagne d'Arc d'Est. Cela a formé un groupe de monophylétique avec le sous lignage de S4 du lac Malawi (l'identité de pourcentage de 95,4 à 96,8%) et a différé du sous lignage de S4 du lac Victoria par 4,5%. La coexistence dans le même champ de S4, S5 et S6 a été observé dans la région de Montagnes d'Arc d'Est. La forte compétition entre les variantes de RYMV a été soupçonnée de par la distribution limitée de S5. Cette étude confirme des spéculations que la région de Montagne d'Arc d'est est le centre d'origine de RYMV. Ainsi, le haut chargement viral dans la Montagne d'Arc de l'Est implique que c'est un emplacement convenable pour les études stratégiques visées à concevoir d'interventions de contrôle contre RYMV

Lithospheric structural control on inversion of the southern margin of the Black Sea Basin, Central Pontides, Turkey

International audienc

Cross-sectional anatomy and geodynamic evolution of the Central Pontide orogenic belt (northern Turkey)

International audienceGeophysical data allowed the construction of a ~250-km-long lithospheric-scale balanced cross section of the southern Black Sea margin (Espurt et al. 2014). In this paper we combine structural field data, stratigraphic data, and fault kinematics analyses with the 70 km-long onshore part of the section to reconstruct the geodynamic evolution of the Central Pontide orogen. These data reveal new aspects of the structural evolution of the Pontides since the Early Cretaceous. The Central Pontides is a doubly vergent orogenic wedge that results from the inversion of normal faults. Extensional subsidence occurred with an ENE-trend from Aptian to Paleocene in a forearc setting. We infer that the Black Sea back-arc basin also opened during this period, which was also the period of subduction of the Tethys Ocean below the Pontides. As in the Western Pontides, the Cretaceous-Paleocene subsidence was interrupted from Latest Albian to Coniacian time by uplift and erosion that was probably related to a block collision and accretion in the subduction zone. The restoration of the section to its pre-shortening state (Paleocene) shows that fault-related subsidence locally reached 3600 m within the forearc basin. Structural inversion occurred from Early Eocene to Mid-Miocene as a result of collision and indentation of the Pontides by the Kırşehir continental block to the south, with 27.5 km (~28%) shortening along the section studied. The inversion was characterized by NNE-trending shortening that predated the Late Neogene dextral escape of Anatolia along the North Anatolian Fault and the modern stress field characterized by NW-trending compression within the Eocene Boyabat basin