Incidence rate and predictors of COVID-19 in the two largest cities of Burkina Faso - prospective cohort study in 2021 (ANRS-COV13).

BACKGROUND: Early data on COVID-19 (based primarily on PCR testing) indicated a low burden in Sub-Saharan Africa. To better understand this, this study aimed to estimate the incidence rate and identify predictors of SARS-CoV-2 seroconversion in the two largest cities of Burkina Faso. This study is part of the EmulCOVID-19 project (ANRS-COV13). METHODS: Our study utilized the WHO Unity protocol for cohort sero-epidemiological studies of COVID-19 in general population. We conducted random sampling stratified by age group and sex. Individuals aged 10 years and older in the cities of Ouagadougou and Bobo-Dioulasso, Burkina Faso were included and surveyed at 4 time points, each 21 days apart, from March 3 to May 15, 2021. WANTAI SARS-CoV-2 Ab ELISA serological tests were used to detect total antibodies (IgM, IgG) in serum. Predictors were investigated using Cox proportional hazards regression. RESULTS: We analyzed the data from 1399 participants (1051 in Ouagadougou, 348 in Bobo-Dioulasso) who were SARS-CoV-2 seronegative at baseline and had at least one follow-up visit. The incidence rate of SARS-CoV-2 seroconversion was 14.3 cases [95%CI 13.3-15.4] per 100 person-weeks. The incidence rate was almost three times higher in Ouagadougou than in Bobo-Dioulasso (Incidence rate ratio: IRR = 2.7 [2.2-3.2], p < 0.001). The highest incidence rate was reported among women aged 19-59 years in Ouagadougou (22.8 cases [19.6-26.4] per 100 person-weeks) and the lowest among participants aged 60 years and over in Bobo-Dioulasso, 6.3 cases [4.6-8.6] per 100 person-weeks. Multivariable analysis showed that participants aged 19 years and older were almost twice as likely to seroconvert during the study period compared with those aged 10 to 18 years (Hazard ratio: HR = 1.7 [1.3-2.3], p < 0.001). Those aged 10-18 years exhibited more asymptomatic forms than those aged 19 years and older, among those who achieved seroconversion (72.9% vs. 40.4%, p < 0.001). CONCLUSION: The spread of COVID-19 is more rapid in adults and in large cities. Strategies to control this pandemic in Burkina Faso, must take this into account. Adults living in large cities should be the priority targets for vaccination efforts against COVID-19.

KIR2DL5B and HLA DRB1*12 alleles seems to be associated with protection against HIV-1 in serodiscordant couples in Burkina Faso.

The human immunodeficiency virus (HIV) belongs to the Retroviridae family and remains a public health problem in sub-Saharan Africa. Recent reports from WHO have shown that 33 million people died from HIV infections. HIV is one of the most serious fatal human diseases of the 20th and 21st centuries. However, variations in genetic and immunological factors are associated with protection against HIV infection in uninfected people exposed to HIV. This is the case with naturals killers which play an important role in the progression or regression of HIV infection. The objective of this study is to characterize certain HLA (human leukocyte antigen) class II genes and KIR genes in HIV-1 serodiscordant couples in Burkina Faso. This study was carried out at Burkina Faso among nineteen (19) HIV-1 serodiscordant couples. Classical multiplex PCR (SSP-PCR) was used to characterize the presence or absence of the KIR genes and certain class II HLAs (DRB1*11 and DRB1*12). The characterization of the KIR and HLA genes DRB1*11, DRB1*12 in this study demonstrated that the inhibitor KIR2DL5B, would confer protection against HIV-1 infection in seronegative partners (odd ratio [OR] = 0.13 [0.02-0.72] and p = 0.029), and the HLA DRB1*12 allele was associated with protection against HIV-1 infection in seronegative partners (OR = 0.16 [0.03-0.77] and p = 0.038). AA and Bx haplotypes were not found to be associated with HIV-1 infection in serodiscordant couples. This study confirms the involvement of the KIR genes in viral pathologies such as HIV-1 infection. Future larger-scale studies may provide a better understanding of the molecular mechanism by which the KIR haplotype and combination of KIR/HLA are associated with protection against HIV infection.

Cervical cancer in the Hauts-Bassins region of Burkina Faso: Results of a screening campaign by visual inspection with acetic acid (VIA screening in Burkina Faso).

This study was conducted to describe the distribution of precancerous and cancerous lesions of the cervix uteri, enumerated during a mass screening in Burkina Faso. We conducted a cross-sectional study involving 577 women aged 18 to 60 years, carried out from November 23 to December 19, 2013, in the city of Bobo-Dioulasso and in the rural commune of Bama. Regarding the screening results, 89 participants (15.4%) were positive for pre-malignant cervical lesions. Chi-square testing and logistic regression analyses were conducted to identify the likelihood of cervical pre-cancer lesion in the women. Participants less than 29 years old were approximately 3 times more likely to have cervical lesions than participants >39 years. Participants who were parous (1-3 deliveries) and multiparous (four or more deliveries) were approximately 4 times more likely to present with cervical lesions than nulliparous women. Access to screening services is low in the Bobo-Dioulasso region. Further research should be conducted to understand the incidence and distribution of cervical precancerous and cancerous lesions in Burkina Faso.

Estimating the Force of Infection for Dengue Virus Using Repeated Serosurveys, Ouagadougou, Burkina Faso.

Because of limited data on dengue virus in Burkina Faso, we conducted 4 consecutive age-stratified longitudinal serologic surveys, ≈6 months apart, among persons 1-55 years of age, during June 2015-March 2017, which included a 2016 outbreak. The seroconversion rate before the serosurvey enrollment was estimated by binomial regression, taking age as the duration of exposure, and assuming constant force of infection (FOI) over age and calendar time. We calculated FOI between consecutive surveys and rate ratios for potentially associated characteristics based on seroconversion using the duration of intervals. Among 2,897 persons at enrollment, 66.3% were IgG-positive, and estimated annual FOI was 5.95%. Of 1,269 enrollees participating in all 4 serosurveys, 438 were IgG-negative at enrollment. The annualized FOI ranged from 10% to 20% (during the 2016 outbreak). Overall, we observed high FOI for dengue. These results could support decision-making about control and preventive measures for dengue.

Leptospirosis as Cause of Febrile Icteric Illness, Burkina Faso.

Patients in Burkina Faso who sought medical attention for febrile jaundice were tested for leptospirosis. We confirmed leptospirosis in 27 (3.46%) of 781 patients: 23 (2.94%) tested positive using serologic assays and 4 (0.51%) using LipL32 PCR. We further presumed leptospirosis in 16 (2.82%) IgM-positive specimens.

Estimation of HIV-1 DNA Level Interfering with Reliability of HIV-1 RNA Quantification Performed on Dried Blood Spots Collected from Successfully Treated Patients.

The impact of HIV-1 DNA coamplification during HIV-1 RNA quantification on dried blood spots (DBS) was explored. False-positive HIV RNA detection (22/62, 35%) was associated with high HIV-1 DNA levels. Specificity of HIV-1 RNA assays on DBS should be evaluated following manufacturer protocols on samples with HIV-1 DNA levels of ≥1,000 copies/10(6) peripheral blood mononuclear cells.

Co-circulation of two Alphaviruses in Burkina Faso: Chikungunya and O'nyong nyong viruses.

BACKGROUND: Chikungunya virus (CHIKV) and O'nyong nyong virus (ONNV) are phylogenetically related alphaviruses in the Semliki Forest Virus (SFV) antigenic complex of the Togaviridae family. There are limited data on the circulation of these two viruses in Burkina Faso. The aim of our study was to assess their circulation in the country by determining seroprevalence to each of the viruses in blood donor samples and by retrospective molecular and serological testing of samples collected as part of national measles and rubella surveillance. METHODOLOGY/PRINCIPAL FINDINGS: All blood donor samples were analyzed on the Luminex platform using CHIKV and ONNV E2 antigens. Patient samples collected during national measles-rubella surveillance were screened by an initial ELISA for CHIKV IgM (CHIKjj Detect IgM ELISA) at the national laboratory. The positive samples were then analyzed by a second ELISA test for CHIKV IgM (CDC MAC-ELISA) at the reference laboratory. Finally, samples that had IgM positive results for both ELISA tests and had sufficient residual volume were tested by plaque reduction neutralization testing (PRNT) for CHIKV and ONNV. These same patient samples were also analyzed by rRT-PCR for CHIKV. Among the blood donor specimens, 55.49% of the samples were positive for alphaviruses including both CHIKV and ONNV positive samples. Among patient samples collected as part of national measles and rubella surveillance, 3.09% were IgM positive for CHIKV, including 2.5% confirmed by PRNT. PRNT failed to demonstrate any ONNV infections in these samples. No samples tested by RT-qPCR. had detectable CHIKV RNA. CONCLUSIONS/SIGNIFICANCE: Our results suggest that CHIKV and ONNV have been circulating in the population of Burkina Faso and may have been confused with malaria, dengue fever or other febrile diseases such as measles or rubella. Our study underscores the necessity to enhance arbovirus surveillance systems in Burkina Faso.

Multicountry study of SARS-CoV-2 and associated risk factors among healthcare workers in Côte d'Ivoire, Burkina Faso and South Africa.

BACKGROUND: Reports on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread across Africa have varied, including among healthcare workers (HCWs). This study assessed the comparative SARS-CoV-2 burden and associated risk factors among HCWs in three African countries. METHODS: A multicentre study was conducted at regional healthcare facilities in Côte d'Ivoire (CIV), Burkina Faso (BF) and South Africa (SA) from February to May 2021. HCWs provided blood samples for SARS-CoV-2 serology and nasopharyngeal/oropharyngeal swabs for testing of acute infection by polymerase chain reaction and completed a questionnaire. Factors associated with seropositivity were assessed with logistic regression. RESULTS: Among 719 HCWs, SARS-CoV-2 seroprevalence was 34.6% (95% confidence interval 31.2 to 38.2), ranging from 19.2% in CIV to 45.7% in BF. A total of 20 of 523 (3.8%) were positive for acute SARS-CoV-2 infection. Female HCWs had higher odds of SARS-CoV-2 seropositivity compared with males, and nursing staff, allied health professionals, non-caregiver personnel and administration had higher odds compared with physicians. HCWs also reported infection prevention and control (IPC) gaps, including 38.7% and 29% having access to respirators and IPC training, respectively, in the last year. CONCLUSIONS: This study was a unique comparative HCW SARS-CoV-2 investigation in Africa. Seroprevalence estimates varied, highlighting distinctive population/facility-level factors affecting COVID-19 burden and the importance of established IPC programmes to protect HCWs and patients.

Screening of Circulation of Usutu and West Nile Viruses: A One Health Approach in Humans, Domestic Animals and Mosquitoes in Burkina Faso, West Africa.

Usutu virus (USUV) and West Nile virus (WNV) are phylogenetically closely related arboviruses. These viruses mainly follow an enzootic cycle involving mosquitoes and birds, but they occasionally infect humans and other mammals, inducing neurotropic disorders. Since the discovery of USUV, only two human cases have been reported in Africa, including one in Burkina Faso in 2004. Since then, no studies have been conducted to measure the extent of the circulation of this virus in Burkina Faso, and no study regarding the circulation of WNV has been conducted. Our study aimed to determine the seroprevalence of USUV and WNV in blood donations and in animals (horses, dogs, chickens and pigeons) and to perform molecular screening in patients with febrile fever and in Culex quinquefasciatus and Aedes aegypti mosquitoes. The prevalence of USUV and WNV was studied by serological (ELISA and microneutralization tests) and molecular analyses (RT-qPCR) of mosquito, dog, domestic bird, horse, and human samples in Burkina Faso between 2019 and 2021. We detected a very active transmission of both viruses in Burkina Faso. WNV and USUV seroprevalence is particularly high in humans (19.16% and 14.17%, respectively) and horses (17.28% and 6.17%). Molecular screening did not detect WNV or USUV in the mosquito or human samples tested. Our study shows an active spread of USUV and WNV in Burkina Faso, especially for WNV. This study highlights the value of developing surveillance programs to better prevent, detect, and alert people to USUV and WNV circulation in both primary and incidental hosts.

[Dengue virus circulation in West Africa: An emerging public health issue]. / Circulation du virus de la dengue en Afrique de l'Ouest - Une problématique émergente de santé publique.

Dengue is the most widespread arbovirosis in the world, with approximately 390 million cases per year, 96 millions of which have clinical manifestations and 25,000 deaths. In West Africa, the circulation of this virus in human populations was first reported in the 1960s in Nigeria. Clinical diagnosis of dengue in West Africa is made difficult by the existence of other diseases with similar clinical presentations. Biological diagnosis remains therefore the only alternative. This biological diagnosis requires high quality equipment and well-trained personnel, which are not always available in resource-limited countries. Thus, many cases of dengue fever are consistently reported as malaria, leading to mismanagement, which can have serious consequences on the health status of patients. It is therefore necessary to set up surveillance systems for febrile infections of unknown origin in Africa by strengthening the diagnostic capacities of national laboratories.

TITLE: Circulation du virus de la dengue en Afrique de l'Ouest - Une problématique émergente de santé publique. ABSTRACT: La dengue est l'arbovirose la plus répandue dans le monde avec environ 390 millions de cas par an, dont 96 millions présentent des manifestations cliniques, avec plus de 25 152 décès annuels répertoriés. Le diagnostic clinique de la dengue en Afrique de l'Ouest est rendu difficile par l'existence d'autres maladies présentant des tableaux cliniques similaires. Il est donc nécessaire de mettre en place des systèmes de surveillance des infections fébriles d'origine inconnue en Afrique, en renforçant les capacités diagnostiques des laboratoires nationaux.

Serological Evidence of Zika Virus Circulation in Burkina Faso.

Zika virus (ZIKV) and dengue virus (DENV) are two closely related members of the Flaviviridae family, both transmitted by mosquitoes of the genus Aedes, and are among the arboviruses most at risk to human health. Burkina Faso has been facing an upsurge in DENV outbreaks since 2013. Unlike DENV, there is no serological evidence of ZIKV circulation in humans in Burkina Faso. The main objective of our study was to determine the seroprevalence of ZIKV and DENV in blood donors in Burkina Faso. A total of 501 donor samples collected in the two major cities of the country in 2020 were first tested by a competitive enzyme-linked immunosorbent assay to detect flavivirus antibodies. Positive sera were then tested using Luminex to detect ZIKV and DENV antibodies and virus-specific microneutralization tests against ZIKV were performed. The ZIKV seroprevalence was 22.75% in the donor samples and we found seropositivity for all DENV-serotypes ranging from 19.56% for DENV-1 to 48.86% for DENV-2. Molecular analyses performed on samples from febrile patients and Aedes aegypti mosquitoes between 2019 and 2021 were negative. Our study showed the important circulation of ZIKV and DENV detected by serology although molecular evidence of the circulation of ZIKV could not be demonstrated. It is essential to strengthen existing arbovirus surveillance in Burkina Faso and more broadly in West Africa by focusing on fevers of unknown origin and integrating vector surveillance to assess the extent of ZIKV circulation and identify the circulating strain. Further studies are needed to better understand the epidemiology of this virus in order to define appropriate prevention and response methods.

Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions.

The metabolome is a central determinant of human phenotypes and includes the plethora of small molecules produced by host and microbiome or taken up from exogenous sources. However, studies of the metabolome have so far focused predominantly on urban, industrialized populations. Through an untargeted metabolomic analysis of 90 fecal samples from human individuals from Africa and the Americas-the birthplace and the last continental expansion of our species, respectively-we characterized a shared human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the shared human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features such as amino acid-conjugated bile acids and urobilin as major metabolic correlates of these behavioral shifts. Additionally, coanalyses with over 5,000 publicly available human fecal samples and cooccurrence probability analyses with the gut microbiome highlight connections between the human fecal metabolome and gut microbiome. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a shared human fecal metabolome. This study represents the first characterization of the shared human fecal metabolome through untargeted analyses of populations along an industrialization gradient. IMPORTANCE As the world becomes increasingly industrialized, understanding the biological consequences of these lifestyle shifts and what it means for past, present, and future human health is critical. Indeed, industrialization is associated with rises in allergic and autoimmune health conditions and reduced microbial diversity. Exploring these health effects on a chemical level requires consideration of human lifestyle diversity, but understanding the significance of any differences also requires knowledge of what molecular components are shared between human groups. Our study reveals the key chemistry of the human gut as defined by varied industrialization-based differences and ubiquitous shared features. Ultimately, these novel findings extend our knowledge of human molecular biology, especially as it is influenced by lifestyle and behavior, and provide steps toward understanding how human biology has changed over our species' history.

Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle.

High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2-5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.

Laboratory capacity assessments in 25 African countries at high risk of yellow fever, August-December 2018.

INTRODUCTION: accurate and timely laboratory diagnosis of yellow fever (YF) is critical to the Eliminate Yellow Fever Epidemics (EYE) strategy. Gavi, the Vaccine Alliance recognized the need to support and build capacity in the national and regional laboratories in the Global YF Laboratory Network (GYFLN) as part of this strategy. METHODS: to better understand current capacity, gaps and needs of the GYFLN laboratories in Africa, assessments were carried out in national and regional reference laboratories in the 25 African countries at high risk for YF outbreaks that were eligible for new financial support from Gavi. RESULTS: the assessments found that the GYFLN in Africa has high capacity but 21% of specimens were not tested due to lack of testing kits or reagents and approximately 50% of presumptive YF cases were not confirmed at the regional reference laboratory due to problems with shipping. CONCLUSION: the laboratory assessments helped to document the baseline capacities of these laboratories prior to Gavi funding to support strengthening YF laboratories.

Low prevalence rate of indeterminate serological human immunodeficiency virus results among pregnant women from Burkina Faso, West Africa.

Rapid human immunodeficiency virus (HIV) antibody tests have been adopted into national guidelines for HIV testing in many countries in sub-Saharan Africa. One goal of HIV rapid testing is to minimize the occurrence of indeterminate results. From January 2005 to December 2007, plasma (or serum) samples from pregnant women in Bobo-Dioulasso (Burkina Faso, West Africa) were screened for HIV by using two rapid tests (the Determine HIV1/2 test [Abbott] and Genie II HIV-1/HIV-2 [Bio-Rad]) through a sequential algorithm prior to enrollment of HIV-1-infected women in a prevention of mother-to-child transmission (PMTCT) trial (WHO/ANRS 1289 Kesho Bora trial). Samples exhibiting indeterminate results (Determine positive and Genie II negative) were further tested with a fourth-generation HIV enzyme immunoassay (EIA) (Murex HIV Ag/Ab combination in 2005 and 2006 and Vironostika HIV Uni-Form II Ag/Ab in 2007). If positive, they were finally assessed for HIV-1 RNA (Generic HIV-1 RNA viral load assay; Biocentric). From a total of 44,653 samples tested, 597 (1.3%) showed indeterminate results. Of these, 367 could be analyzed by EIA. Only 15 (15/367, 4.1%) samples were found EIA reactive. Of these, 11 could be tested for HIV-1 RNA. All were HIV-1 RNA negative. In our clinical practice, pregnant women with such indeterminate results are now reassured during posttest counseling that they are very unlikely to be infected with HIV-1. As a consequence, such women with indeterminate results can reliably be considered negative when urgent clinical decisions (such as providing PMTCT prophylaxis) need to be taken.

Analytical performance of eight rapid point-of-care tests routinely used for the detection of HBsAg in Burkina Faso: A cross-sectional study.

BACKGROUND: In limited resources countries, HBsAg-rapid diagnostic test (RDT) represents a good alternative for the diagnosis of hepatitis B virus (HBV) infection. Due to many factors that can influence their analytical performances, an evaluation with local biological samples before using on a large scale is recommended. OBJECTIVES: The aims of the study were: (i) to evaluate the analytical performance of eight commercial RDTs used in Burkina Faso for the detection of HBsAg using serum from blood donors, and (ii) to propose an algorithm using these RDTs based on their analytical performance. STUDY DESIGN: 109 HBsAg-positive and 216 HBsAg-negative samples were included in this evaluation. A modified version of the World Health Organization (WHO) algorithm for the detection of HBsAg was used as the gold standard. A pairwise combination of RDTs performance was done to choose the best diagnostic algorithm. RESULTS: All RDTs presented an excellent specificity (Sp) (≥99.0 %) except Accucare HBsAg® test. Sensitivity (Se) ranged from 90.8 % (95 % CI: 87.9-93.7) for Rapid Signal™ HBsAg to 92.8 % (95 % CI: 90.3-95.5) for SD BioLine® HBsAg and Artron® HBsAg. The pairwise combinations of the Se and Sp of RDTs showed no improvement in diagnostic performance. CONCLUSION: The RDTs evaluated in this study have good sensitivities and excellent specificities indicating their use in clinical practice and for HBV mass screening in Burkina Faso. However, their use should be monitored in the context of blood transfusion. Furthermore, according to our algorithm, each positive sample should be confirmed by another RDT of good Se.

Dengue virus infection and pregnancy outcomes during the 2017 outbreak in Ouagadougou, Burkina Faso: A retrospective cohort study.

INTRODUCTION: Dengue fever is a re-emerging pathology in Burkina Faso. It affects everyone and pregnant women are not left out. The objective of this study was to estimate the burden of dengue fever and to assess its effects on pregnancy outcomes in hospitalized pregnant women during the 2017 outbreak in Ouagadougou, Burkina Faso. METHOD: This was a retrospective cohort study including febrile pregnant women from five health facilities in Ouagadougou. The study was carried out from July 1st to December 31st, 2017. A logistic stepwise regression was performed to identify the pregnancy adverse outcomes risk factors. RESULTS: Our study included 424 pregnant women at a mean age of 27.1 years old (Standard deviation: 6.23 years). Overall 28.54% (121/424) were infected with dengue virus. During follow-up, 29.01% (123/424) presented an adverse pregnancy outcome. Adjusted for gestational age and clinical symptoms, the risk of adverse pregnancy outcome was twice as high among dengue infected women as compared to uninfected women with an adjusted Odds Ratio (aOR) = 2.09 (1.08-4.05). The risk of the adverse pregnancy outcome was higher in the third trimester of pregnancy with aOR = 1.66 (1.02-2.72) in dengue fever infected women. CONCLUSION: Dengue fever is a risk factor for adverse pregnancy outcomes, especially in the third trimester in Burkina Faso. The implementation of effective anti-vectorial control interventions and better management of dengue fever during pregnancy are needed to improve pregnancy outcomes.

Monitoring Insecticide Susceptibility in Aedes Aegypti Populations from the Two Biggest Cities, Ouagadougou and Bobo-Dioulasso, in Burkina Faso: Implication of Metabolic Resistance.

In West Africa, Aedes aegypti remains the major vector of dengue virus. Since 2013, dengue fever has been reemerging in Burkina Faso with annual outbreaks, thus becoming a major public health problem. Its control relies on vector control, which is unfortunately facing the problem of insecticide resistance. At the time of this study, although data on phenotypic resistance were available, information related to the metabolic resistance in Aedes populations from Burkina Faso remained very scarce. Here, we assessed the phenotypic and the metabolic resistance of Ae. aegypti populations sampled from the two main urban areas (Ouagadougou and Bobo-Dioulasso) of Burkina Faso. Insecticide susceptibility bioassays to chlorpyriphos-methyl 0.4%, bendiocarb 0.1% and deltamethrin 0.05% were performed on natural populations of Ae. aegypti using the WHO protocol. The activity of enzymes involved in the rapid detoxification of insecticides, especially non-specific esterases, oxidases (cytochrome P450) and glutathione-S-transferases, was measured on individual mosquitos. The mortality rates for deltamethrin 0.05% were low and ranged from 20.72% to 89.62% in the Bobo-Dioulasso and Ouagadougou sites, respectively. When bendiocarb 0.1% was tested, the mortality rates ranged from 7.73% to 71.23%. Interestingly, in the two urban areas, mosquitoes were found to be fully susceptible to chlorpyriphos-methyl 0.4%. Elevated activity of non-specific esterases and glutathione-S-transferases was reported, suggesting multiple resistance mechanisms involved in Ae. aegypti populations from Bobo-Dioulasso and Ouagadougou (including cytochrome P450). This update to the insecticide resistance status within Ae. aegypti populations in the two biggest cities is important to better plan dengue vectors control in the country and provides valuable information for improving vector control strategies in Burkina Faso, West Africa.

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content.

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.