Dataset Information

Full Genome Characterization of a New Simian Immune Deficiency Virus Lineage in a Naturally Infected Cercopithecus ascanius whitesidei in the Democratic Republic of Congo Reveals High Genetic Diversity Among Red-Tailed Monkeys in Central and Eastern Africa.

ABSTRACT: Our knowledge on simian immune deficiency virus (SIV) diversity and evolution in the different nonhuman primate species is still incomplete. In this study, we report the full genome characterization of a new SIV from a red-tailed monkey (2013DRC-I8), from the Cercopithecus ascanius whitesidei subspecies, in the Democratic Republic of Congo (DRC). The new full-length genome is 9,926?bp long, and the genomic structure is similar to that of other SIVs with the absence of vpx and vpu genes. The new SIVasc-13DRC-I8 strain fell within the Cercopithecus specific SIV lineage. SIVasc-13DRC-I8 and previously reported SIVrtg from the C.a. schmidti subspecies in Uganda did not form a separate species-specific SIV lineage. These observations provide additional evidence for high genetic diversity and the complex evolution of SIVs in the Cercopithecus genus. More studies on a large number of monkeys from a wider geographic area are needed to understand SIV evolution.

SUBMITTER: Ahuka-Mundeke S

PROVIDER: S-EPMC5512325 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Full Genome Characterization of a New Simian Immune Deficiency Virus Lineage in a Naturally Infected Cercopithecus ascanius whitesidei in the Democratic Republic of Congo Reveals High Genetic Diversity Among Red-Tailed Monkeys in Central and Eastern Africa.

Ahuka-Mundeke Steve S Mbala-Kingebeni Placide P Ndimbo-Kumogo Simon-Pierre SP Foncelle Caroline C Lunguya-Metila Octavie O Muyembe-Tamfum Jean-Jacques JJ Delaporte Eric E Peeters Martine M Ayouba Ahidjo A

AIDS research and human retroviruses 20170406 7

Our knowledge on simian immune deficiency virus (SIV) diversity and evolution in the different nonhuman primate species is still incomplete. In this study, we report the full genome characterization of a new SIV from a red-tailed monkey (2013DRC-I8), from the Cercopithecus ascanius whitesidei subspecies, in the Democratic Republic of Congo (DRC). The new full-length genome is 9,926 bp long, and the genomic structure is similar to that of other SIVs with the absence of vpx and vpu genes. The new ...[more]

PMID: 28383997

Similar Datasets

Project description:An increase of congenital anomalies in the eastern Democratic Republic of the Congo (DRC) has been reported. Congenital malformations (CMs) are not uncommon among newborns and, if left untreated, can contribute to increased neonate morbidity and mortality.Medical records of all individuals admitted with a diagnosed CM to HEAL Africa Teaching Hospital (Goma, DRC) from 2002 to 2014 (n=1301) were reviewed. Data were analysed using descriptive statistics to summarize chart records, and inferential statistics to investigate significant barriers to earlier treatment.Since 2012, the number of patients treated each year for CMs has increased by over 200% compared to the average annual number of cases treated from 2002-2011. Though delayed presentation of patients to HEAL Hospital was very obvious, with an average age of 8.2 years. We find that patient age has been significantly decreasing (p=0.037) over time. The average distance separating patients from HEAL Hospital was 178 km, with approximately one third living 350 km or further from the treatment center. Distance is the most significant (p=3.33x10(-6)) barrier to earlier treatment. When controlling for an interaction between gender and the use of mercy funds, we also find that female patients are at a significant (p=1.04x10(-3)) disadvantage to undergo earlier corrective surgery. This disadvantage is further illustrated by our finding that 89% of women and girls, and over 81% of all patients, required mercy funds to cover the cost of surgery in 2014. Lastly, the mortality rate for surgery was low and averaged less than 1.0%.Despite a formal end to the war in 2009, and an overall increase in individuals undergoing corrective surgery, distance, poverty, and gender are still massive barriers to CM care at HEAL Hospital, Goma, DRC. We find that patients have been successfully treated earlier by HEAL, although the average age of CM correction in 2014 (4.9 years) is still above average for Sub-Saharan Africa. Thus, we advocate for further funding from the National Government and international health agencies to enable continued treatment of CMs in rural residents of the eastern DRC. Distance, the most significant barrier to care can be mitigated by the implementation of additional mobile clinics and the construction of regional surgery centers along with the associated hiring of surgeons trained in CM repair.

Project description:BackgroundReducing morbidity is the main target of schistosomiasis control efforts, yet only rarely do control programmes assess morbidity linked to Schistosoma sp. infection. In the Democratic Republic of Congo (DRC), and particularly in north-eastern Ituri Province, little is known about morbidity associated with Schistosoma mansoni infection. For this reason, we aimed to assess intestinal and hepatosplenic morbidity associated with S. mansoni infection in Ituri Province.Methods/principal findingsIn 2017, we conducted a cross-sectional study in 13 villages in Ituri Province, DRC. S. mansoni infection was assessed with a Kato-Katz stool test (2 smears) and a point-of-care circulating cathodic antigen (POC-CCA) urine test. A questionnaire was used to obtain demographic data and information about experienced intestinal morbidity. Each participant underwent an abdominal ultrasonography examination to diagnose hepatosplenic morbidity. Of the 586 study participants, 76.6% tested positive for S. mansoni. Intestinal morbidity reported in the two preceding weeks was very frequent, and included abdominal pain (52.7%), diarrhoea (23.4%) and blood in the stool (21.5%). Hepatosplenic morbidity consisted of abnormal liver parenchyma patterns (42.8%), hepatomegaly (26.5%) and splenomegaly (25.3%). Liver pathology (adjusted odds ratio [aOR] 1.20, 95% confidence interval [CI] 1.06-1.37, p = 0.005) was positively and significantly associated with S. mansoni infection. Hepatomegaly (aOR 1.52, 95% CI 0.99-2.32, p = 0.053) and splenomegaly (aOR 1.12, 95% CI 0.73-1.72, p = 0.619) were positively but not significantly associated with S. mansoni infection at the individual level. At the village level, S. mansoni prevalence was positively associated with the prevalence of hepatomegaly and splenomegaly. High-intensity S. mansoni infections were associated with diarrhoea, blood in the stool, hepatomegaly, splenomegaly, and liver parenchyma (C, D, E and F pathology patterns). Four study participants were diagnosed with ascites and five reported hematemesis.Conclusions/significanceOur study documents a high burden of intestinal and hepatosplenic morbidity associated with S. mansoni infection status in Ituri Province. The findings call for targeted interventions to address both S. mansoni infection and related morbidity.

Project description:BackgroundMalaria vector control in the Democratic Republic of the Congo is plagued by several major challenges, including inadequate infrastructure, lack of access to health care systems and preventative measures, and more recently the widespread emergence of insecticide resistance among Anopheles mosquitoes. Across 26 provinces, insecticide resistance has been reported from multiple sentinel sites. However, to date, investigation of molecular resistance mechanisms among Anopheles vector populations in DRC has been more limited.MethodsAdult Anopheles gambiae sensu lato (s.l.) and Anopheles funestus s.l. were collected from two sites in Sud-Kivu province and one site in Haut-Uélé province and PCR-screened for the presence of 11 resistance mutations, to provide additional information on frequency of resistance mechanisms in the eastern DRC, and to critically evaluate the utility of these markers for prospective country-wide resistance monitoring.ResultsL1014F-kdr and L1014S-kdr were present in 75.9% and 56.7% of An. gambiae s.l. screened, respectively, with some individuals harbouring both resistant alleles. Across the three study sites, L43F-CYP4J5 allele frequency ranged from 0.42 to 0.52, with evidence for ongoing selection. G119S-ace1 was also identified in all sites but at lower levels. A triple mutant haplotype (comprising the point mutation CYP6P4-I236M, the insertion of a partial Zanzibar-like transposable element and duplication of CYP6AA1) was present at high frequencies. In An. funestus s.l. cis-regulatory polymorphisms in CYP6P9a and CYP6P9b were detected, with allele frequencies ranging from 0.82 to 0.98 and 0.65 to 0.83, respectively.ConclusionsThis study screened the most up-to-date panel of DNA-based resistance markers in An. gambiae s.l. and An. funestus s.l. from the eastern DRC, where resistance data is lacking. Several new candidate markers (CYP4J5, G119S-ace1, the triple mutant, CYP6P9a and CYP6P9b) were identified, which are diagnostic of resistance to major insecticide classes, and warrant future, larger-scale monitoring in the DRC to inform vector control decisions by the National Malaria Control Programme.

Project description:BackgroundSchistosomiasis, caused by Schistosoma mansoni, is of great significance to public health in sub-Saharan Africa. In the Democratic Republic of Congo (DRC), information on the burden of S. mansoni infection is scarce, which hinders the implementation of adequate control measures. We assessed the geographical distribution of S. mansoni infection across Ituri province in north-eastern DRC and determined the prevailing risk factors.Methods/principal findingsTwo province-wide, community-based studies were conducted. In 2016, a geographical distribution study was carried out in 46 randomly selected villages across Ituri. In 2017, an in-depth study was conducted in 12 purposively-selected villages, across the province. Households were randomly selected, and members were enrolled. In 2016, one stool sample was collected per participant, while in 2017, several samples were collected per participant. S. mansoni eggs were detected using the Kato-Katz technique. In 2017, a point-of-care circulating cathodic S. mansoni antigen (POC-CCA) urine test was the second used diagnostic approach. Household and individual questionnaires were used to collect data on demographic, socioeconomic, environmental, behavioural and knowledge risk factors. Of the 2,131 participants in 2016, 40.0% were positive of S. mansoni infection. Infection prevalence in the villages ranged from 0 to 90.2%. Of the 707 participants in 2017, 73.1% were tested positive for S. mansoni. Prevalence ranged from 52.8 to 95.0% across the health districts visited. Infection prevalence increased from north to south and from west to east. Exposure to the waters of Lake Albert and the villages' altitude above sea level were associated with the distribution. Infection prevalence and intensity peaked in the age groups between 10 and 29 years. Preschool children were highly infected (62.3%). Key risk factors were poor housing structure (odds ratio [OR] 2.1, 95% 95% confidence interval [CI] 1.02-4.35), close proximity to water bodies (OR 1.72, 95% CI 1.1-2.49), long-term residence in a community (OR 1.41, 95% CI 1.11-1.79), lack of latrine in the household (OR 2.00, 95% CI 1.11-3.60), and swimming (OR 2.53, 95% CI 1.20-5.32) and washing (OR 1.75, 95% CI 1.10-2.78) in local water bodies.Conclusions/significanceOur results show that S. mansoni is highly endemic and a major health concern in Ituri province, DRC. Infection prevalence and intensity, and the prevailing socioeconomic, environmental, and behavioural risk factors in Ituri reflect intense exposure and alarming transmission rates. A robust plan of action is urgently needed in the province.

Project description:BackgroundSulfadoxine-pyrimethamine (SP) is a cornerstone of malaria chemoprophylaxis and is considered for programmes in the Democratic Republic of Congo (DRC). However, SP efficacy is threatened by drug resistance, that is conferred by mutations in the dhfr and dhps genes. The World Health Organization has specified that intermittent preventive treatment for infants (IPTi) with SP should be implemented only if the prevalence of the dhps K540E mutation is under 50%. There are limited current data on the prevalence of resistance-conferring mutations available from Eastern DRC. The current study aimed to address this knowledge gap.MethodsDried blood-spot samples were collected from clinically suspected malaria patients [outpatient department (OPD)] and pregnant women attending antenatal care (ANC) in four sites in North and South Kivu, DRC. Quantitative PCR (qPCR) was performed on samples from individuals with positive and with negative rapid diagnostic test (RDT) results. Dhps K450E and A581G and dhfr I164L were assessed by nested PCR followed by allele-specific primer extension and detection by multiplex bead-based assays.ResultsAcross populations, Plasmodium falciparum parasite prevalence was 47.9% (1160/2421) by RDT and 71.7 (1763/2421) by qPCR. Median parasite density measured by qPCR in RDT-negative qPCR-positive samples was very low with a median of 2.3 parasites/µL (IQR 0.5-25.2). Resistance genotyping was successfully performed in RDT-positive samples and RDT-negative/qPCR-positive samples with success rates of 86.2% (937/1086) and 55.5% (361/651), respectively. The presence of dhps K540E was high across sites (50.3-87.9%), with strong evidence for differences between sites (p < 0.001). Dhps A581G mutants were less prevalent (12.7-47.2%). The dhfr I164L mutation was found in one sample.ConclusionsThe prevalence of the SP resistance marker dhps K540E exceeds 50% in all four study sites in North and South Kivu, DRC. K540E mutations regularly co-occurred with mutations in dhps A581G but not with the dhfr I164L mutation. The current results do not support implementation of IPTi with SP in the study area.

Project description:Zoonotic transmission of simian retroviruses in Central Africa is ongoing and can result in pandemic human infection. While simian foamy virus (SFV) infection was reported in primate hunters in Cameroon and Gabon, little is known about the distribution of SFV in Africa and whether human-to-human transmission and disease occur. We screened 3,334 plasmas from persons living in rural villages in central Democratic Republic of Congo (DRC) using SFV-specific EIA and Western blot (WB) tests. PCR amplification of SFV polymerase sequences from DNA extracted from buffy coats was used to measure proviral loads. Phylogenetic analysis was used to define the NHP species origin of SFV. Participants completed questionnaires to capture NHP exposure information.Sixteen (0.5%) samples were WB-positive; 12 of 16 were from women (75%, 95% confidence limits 47.6%, 92.7%). Sequence analysis detected SFV in three women originating from Angolan colobus or red-tailed monkeys; both monkeys are hunted frequently in DRC. NHP exposure varied and infected women lived in distant villages suggesting a wide and potentially diverse distribution of SFV infections across DRC. Plasmas from 22 contacts of 8 WB-positive participants were all WB negative suggesting no secondary viral transmission. Proviral loads in the three women ranged from 14 - 1,755 copies/105 cells.Our study documents SFV infection in rural DRC for the first time and identifies infections with novel SFV variants from Colobus and red-tailed monkeys. Unlike previous studies, women were not at lower risk for SFV infection in our population, providing opportunities for spread of SFV both horizontally and vertically. However, limited testing of close contacts of WB-positive persons did not identify human-to-human transmission. Combined with the broad behavioral risk and distribution of NHPs across DRC, our results suggest that SFV infection may have a wider geographic distribution within DRC. These results also reinforce the potential for an increased SFV prevalence throughout the forested regions of Africa where humans and simians co-exist. Our finding of endemic foci of SFV infection in DRC will facilitate longitudinal studies to determine the potential for person-to-person transmissibility and pathogenicity of these zoonotic retroviral infections.

Dataset Information

Full Genome Characterization of a New Simian Immune Deficiency Virus Lineage in a Naturally Infected Cercopithecus ascanius whitesidei in the Democratic Republic of Congo Reveals High Genetic Diversity Among Red-Tailed Monkeys in Central and Eastern Africa.

Publications

Full Genome Characterization of a New Simian Immune Deficiency Virus Lineage in a Naturally Infected Cercopithecus ascanius whitesidei in the Democratic Republic of Congo Reveals High Genetic Diversity Among Red-Tailed Monkeys in Central and Eastern Africa.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets