scholarly journals Insights into the Evolutionary Origin of Mediterranean Sandfly Fever Viruses

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Marco Marklewitz ◽  
David P. Tchouassi ◽  
Christian Hieke ◽  
Verena Heyde ◽  
Baldwyn Torto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rift Valley ◽  
Common Ancestor ◽  
Febrile Illness ◽  
Sub Saharan Africa ◽  
Recent Common Ancestor ◽  
Toscana Virus ◽  
Sister Relationship ◽  
Old World ◽  
Sub Saharan

ABSTRACT Sandfly-transmitted phleboviruses (family Phenuiviridae, order Bunyavirales) are associated with febrile illness and infections of the nervous system in humans. These viruses are almost exclusively found in tropical areas of the New World and restricted to semiarid and temperate zones in the Old World. Here, we discovered seven strains of four previously unknown phleboviruses, named Bogoria virus (BOGV), Embossos virus (EMRV), Kiborgoch virus (KBGV), and Perkerra virus (PERV), as well as the recently discovered Ntepes virus, in sandflies collected in the Kenyan Rift Valley. The genomes have a tripartite organization with conserved termini typical of phleboviruses. LOBV, PERV, and EMBV showed low similarity to known phleboviruses, with less than 55% pairwise amino acid identities in the RNA-directed RNA polymerase (RdRp) proteins, and defined a highly diversified monophyletic clade in sister relationship to the sandfly fever Sicilian serocomplex. All three viruses failed to react with sandfly fever Sicilian virus antisera in recombinant immunofluorescence assays (rIFA), suggesting that the viruses belong to a yet-unknown serogroup. In contrast, KBGV was closely related to Toscana virus (84% identity of RdRp proteins) and shared a most recent common ancestor with the clade comprising sandfly fever Naples and Toscana viruses. KBGV reacted with sandfly fever Naples and Toscana virus antisera in rIFA. The genetic diversity of the detected viruses and their phylogenetic positions implies that the Old World sandfly-borne phleboviruses originated from sub-Saharan Africa. Importantly, our findings suggest that diseases associated with sandfly-borne phlebovirus infections may also affect the Kenyan population. IMPORTANCE Studies on the genetic diversity of arthropod-borne viruses circulating in rural regions can provide critical early indications on new emerging viruses essential for global epidemic preparedness. In this study, we describe the discovery of four phleboviruses in sandflies from the Kenyan Rift Valley. The novel viruses are related to the two medically important serocomplexes, sandfly fever Naples and sandfly fever Sicilian, that are associated with febrile illness and neuroinvasive infections and which were previously not known to occur in sub-Saharan Africa. Knowledge on the occurrence of sandfly-borne phleboviruses in Kenya and elsewhere in Africa can help to decipher their contributions in the etiologies of fevers of unknown origin in patients. Our findings on five genetically diverse phleboviruses detected in Kenya suggest that the common ancestor of Old World phleboviruses existed in sub-Saharan Africa, a hot spot for emerging arboviruses.

scholarly journals Genetic diversity of trypanosome species in tsetse flies (Glossina spp.) in Nigeria

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Judith Sophie Weber ◽  
Sen Claudine Henriette Ngomtcho ◽  
Stephen Saikiu Shaida ◽  
Gloria Dada Chechet ◽  
Thaddeus Terlumun Gbem ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Protected Areas ◽  
National Parks ◽  
Sub Saharan Africa ◽  
Tsetse Flies ◽  
Insect Vector ◽  
Limited Information ◽  
Sub Saharan ◽  
Dynamic Populations

Abstract Background Trypanosomes cause disease in humans and livestock in sub-Saharan Africa and rely on tsetse flies as their main insect vector. Nigeria is the most populous country in Africa; however, only limited information about the occurrence and diversity of trypanosomes circulating in the country is available. Methods Tsetse flies were collected from five different locations in or adjacent to protected areas, i.e. national parks and game reserves, in Nigeria. Proboscis and gut samples were analysed for trypanosome DNA by molecular amplification of the internal transcribed spacer 1 (ITS1) region and part of the trypanosome specific glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) gene. Results The most abundant Trypanosoma species found in the tsetse gut was T. grayi, a trypanosome infecting crocodiles. It was ubiquitously distributed throughout the country, accounting for over 90% of all cases involving trypanosomes. Trypanosoma congolense was detected in gut samples from all locations except Cross River National Park, but not in the proboscis, while T. brucei (sensu lato) was not detected at all. In proboscis samples, T. vivax was the most prominent. The sequence diversity of gGAPDH suggests that T. vivax and T. grayi represent genetically diverse species clusters. This implies that they are highly dynamic populations. Conclusions The prevalence of animal pathogenic trypanosomes throughout Nigeria emphasises the role of protected areas as reservoirs for livestock trypanosomes. The genetic diversity observed within T. vivax and T. grayi populations might be an indication for changing pathogenicity or host range and the origin and consequences of this diversity has to be further investigated.

scholarly journals Febrile Illness Evaluation in a Broad Range of Endemicities (FIEBRE): protocol for a multisite prospective observational study of the causes of fever in Africa and Asia

BMJ Open ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. e035632 ◽  
Author(s):  
Heidi Hopkins ◽  
Quique Bassat ◽  
Clare IR Chandler ◽  
John A Crump ◽  
Nicholas A Feasey ◽  
...  
Keyword(s):  
Social Science ◽  
Blood Sample ◽  
Venous Blood ◽  
Febrile Illness ◽  
Clinical Diagnostics ◽  
Control Measures ◽  
Sub Saharan Africa ◽  
Venous Blood Sample ◽  
Open Access Journals ◽  
Sub Saharan

IntroductionFever commonly leads to healthcare seeking and hospital admission in sub-Saharan Africa and Asia. There is only limited guidance for clinicians managing non-malarial fevers, which often results in inappropriate treatment for patients. Furthermore, there is little evidence for estimates of disease burden, or to guide empirical therapy, control measures, resource allocation, prioritisation of clinical diagnostics or antimicrobial stewardship. The Febrile Illness Evaluation in a Broad Range of Endemicities (FIEBRE) study seeks to address these information gaps.Methods and analysisFIEBRE investigates febrile illness in paediatric and adult outpatients and inpatients using standardised clinical, laboratory and social science protocols over a minimum 12-month period at five sites in sub-Saharan Africa and Southeastern and Southern Asia. Patients presenting with fever are enrolled and provide clinical data, pharyngeal swabs and a venous blood sample; selected participants also provide a urine sample. Laboratory assessments target infections that are treatable and/or preventable. Selected point-of-care tests, as well as blood and urine cultures and antimicrobial susceptibility testing, are performed on site. On day 28, patients provide a second venous blood sample for serology and information on clinical outcome. Further diagnostic assays are performed at international reference laboratories. Blood and pharyngeal samples from matched community controls enable calculation of AFs, and surveys of treatment seeking allow estimation of the incidence of common infections. Additional assays detect markers that may differentiate bacterial from non-bacterial causes of illness and/or prognosticate illness severity. Social science research on antimicrobial use will inform future recommendations for fever case management. Residual samples from participants are stored for future use.Ethics and disseminationEthics approval was obtained from all relevant institutional and national committees; written informed consent is obtained from all participants or parents/guardians. Final results will be shared with participating communities, and in open-access journals and other scientific fora. Study documents are available online (https://doi.org/10.17037/PUBS.04652739).

scholarly journals How old are bacterial pathogens?

2016 ◽  
Vol 283 (1836) ◽  
pp. 20160990 ◽  
Author(s):  
Mark Achtman
Keyword(s):  
Genetic Diversity ◽  
Common Ancestor ◽  
Bacterial Pathogens ◽  
Recent Common Ancestor ◽  
Evolutionary Divergence ◽  
Bacterial Diseases ◽  
Most Recent Common Ancestor ◽  
Anatomically Modern Humans ◽  
H Pylori ◽  
Medical Bacteriology

Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori , which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis , the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis . Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.

scholarly journals Complete Genome Analysis of 33 Ecologically and Biologically Diverse Rift Valley Fever Virus Strains Reveals Widespread Virus Movement and Low Genetic Diversity due to Recent Common Ancestry

2006 ◽  
Vol 81 (6) ◽  
pp. 2805-2816 ◽  
Author(s):  
Brian H. Bird ◽  
Marina L. Khristova ◽  
Pierre E. Rollin ◽  
Thomas G. Ksiazek ◽  
Stuart T. Nichol
Keyword(s):  
Genetic Diversity ◽  
Rift Valley ◽  
Complete Genome ◽  
Rift Valley Fever ◽  
Geographic Origin ◽  
Recent Common Ancestor ◽  
Virus Movement ◽  
Long Distance ◽  
Valley Fever ◽  
Virus Strains

ABSTRACT Rift Valley fever (RVF) virus is a mosquito-borne RNA virus responsible for large explosive outbreaks of acute febrile disease in humans and livestock in Africa with significant mortality and economic impact. The successful high-throughput generation of the complete genome sequence was achieved for 33 diverse RVF virus strains collected from throughout Africa and Saudi Arabia from 1944 to 2000, including strains differing in pathogenicity in disease models. While several distinct virus genetic lineages were determined, which approximately correlate with geographic origin, multiple exceptions indicative of long-distance virus movement have been found. Virus strains isolated within an epidemic (e.g., Mauritania, 1987, or Egypt, 1977 to 1978) exhibit little diversity, while those in enzootic settings (e.g., 1970s Zimbabwe) can be highly diverse. In addition, the large Saudi Arabian RVF outbreak in 2000 appears to have involved virus introduction from East Africa, based on the close ancestral relationship of a 1998 East African virus. Virus genetic diversity was low (∼5%) and primarily involved accumulation of mutations at an average of 2.9 × 10−4 substitutions/site/year, although some evidence of RNA segment reassortment was found. Bayesian analysis of current RVF virus genetic diversity places the most recent common ancestor of these viruses in the late 1800s, the colonial period in Africa, a time of dramatic changes in agricultural practices and introduction of nonindigenous livestock breeds. In addition to insights into the evolution and ecology of RVF virus, these genomic data also provide a foundation for the design of molecular detection assays and prototype vaccines useful in combating this important disease.

scholarly journals The epidemiology of febrile illness in sub-Saharan Africa: implications for diagnosis and management

2018 ◽  
Vol 24 (8) ◽  
pp. 808-814 ◽  
Author(s):  
M.J. Maze ◽  
Q. Bassat ◽  
N.A. Feasey ◽  
I. Mandomando ◽  
P. Musicha ◽  
...  
Keyword(s):  
Febrile Illness ◽  
Sub Saharan Africa ◽  
Diagnosis And Management ◽  
Sub Saharan

scholarly journals Genetic Diversity and Allelic Frequency of Glutamate-Rich Protein (GLURP) in Plasmodium falciparum Isolates from Sub-Saharan Africa

2014 ◽  
Vol 7 ◽  
pp. MBI.S20618 ◽  
Author(s):  
Kimberley C. Duru ◽  
Bolaji N. Thomas
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Allelic Diversity ◽  
Allelic Frequency ◽  
Sub Saharan Africa ◽  
Pcr Analysis ◽  
Nested Polymerase Chain Reaction ◽  
Adequate Treatment ◽  
Sub Saharan ◽  
High Degree

Glutamate-rich protein is a Plasmodium falciparum ( Pf) antigen found in all stages of the parasite and has been reported to induce clinical immunity. The R0 and R2 regions have been found to exhibit a high degree of conservation, therefore serving as a good vaccine design material. We assayed the genetic diversity of Pf glurp genes in the R0 and R2 regions, as well as evaluated the role of seasonality on allelic frequency. A total of 402 genomic DNA samples, extracted from filter paper blood samples, were screened by nested polymerase chain reaction (PCR) analysis of Pf glurp R0 and R2 regions, in addition to fragment analysis of the polymorphic regions to identify allelic diversity of the parasite population. We found an extensive heterogeneity in the R2 region in general, and this heterogeneity is seasonally dependent, indicative of region plasticity. The R0 region displayed genetic conservation, as expected. We conclude that positive genotyping results with glurp R0 region should be seen as indicative of an active Pf infection, requiring adequate treatment. In addition, we advocate extending the possibility that an R0 region genotypic positivity could serve as diagnostic tool, thereby reducing cases of untreated or poorly treated infection, contributory to recrudescence or treatment failure.

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