Comparison of Two Molecular Diagnostic Tests for COVID-19: Abbott RealTime SARS-CoV-2 and Allplex™2019-nCoV, in the Epidemic Context in Senegal

Background: The persistence of the rapid spread of the COVID-19 pandemic is linked to the appearance of several variants of SARS-CoV2 with an impact on biological diagnosis, treatment and vaccination. The United States Food and Drug Administration (FDA) has granted several SARS-CoV-2 detection tests Emergency Use Authorization (EUA) for diagnosis and better epidemiological surveillance. Thus, multiple RT-PCR tests have been developed and brought to market in order to meet the urgent need for the diagnosis of COVID-19. However, comparative data between these tests in clinical laboratories are scarcely available to assess their performance. Objective: To compare two molecular methods for detecting SARS-CoV-2: the RT-PCR, Allplex™2019-nCoV tests on CFX96 Bio-Rad and the Abbott m2000sp/rt RealTime SARS-CoV-2. Materials and Methods: Nasopharyngeal and oropharyngeal swabs were taken from patients to diagnose SARS-CoV-2 infection. For each sample, we searched for the virus with two different RT-PCR tests: 1) first on Abbott m2000 SARS-CoV-2 targeting the N and RdRp genes, 2) then on Allplex™2019-nCoV Assay looking for the E, N and RdRp genes. Results: Percentages of the agreement were calculated. A total of 100 samples that tested negative and 90 positives on Abbott m2000 SARS-CoV-2 were retested on Allplex™2019-nCoV. Overall agreement was 74.74% on all samples. The specific agreement was 84% and 64.4% respectively for negative and positive samples with the RealTime SARS-CoV-2 test. A positive correlation (r2 = 0.63;p Conclusion: Our results showed good overall agreement between RT-PCR, Allplex™2019-nCoV and Abbott RealTime SARS-CoV-2 tests in the diagnosis of COVID-19. As the concordance is low for small viremias, the RT-PCR Allplex™2019-nCoV Assay would be better indicated during the acute and symptomatic phase of the disease.

Molecular Genotyping of Human Papillomavirus (HPV) in Hypopharyngeal Cancer

Background: In recent years, head and neck cancers have become common worldwide, ranking sixth in incidence. In 2007, in France the incidence increased by 14,697 including 11,158 among men, which places them in fourth place. The same year, 32,268 patients were hospitalized for this pathology, but 95% are associated with alcohol and tobacco poisoning. Few data exist on these cancers in Africa and Senegal. In recent years, many studies have hypothesized that about 25% of head and neck cancers are associated with high-risk oncogenic human papillomaviruses (HPV) whose role in cervical cancer was already widely established. Objective: To know the prevalence and genotypes of HPV in head and neck cancers, particularly hypopharyngeal cancer. Material and method: This study was carried out on samples of biopsies of hypopharynx cancerous tissue (ulcerative-budding lesion) and healthy oropharyngeal tissue obtained from the ENT department of the Fann hospital, then sent to the Molecular Biology Unit of the Ouakam military hospital (HMO). The nucleic acids extraction was carried out using the standard method of the Zymo research kit “Quick-DNATM Miniprep Plus kit” https://www.zymoresearch.com/. Molecular HPV detection and genotyping were performed by multiplex RT-PCR with the Seegene AnyplexTM II HPV28 kit Detection on a Biorad CFX96 automaton according to the manufacturer’s protocol for the simultaneous genotyping of 28 types of HPV including 19 at High Risk (HR) and 9 low risk (LR). Results: 156 patients were sampled, 61 Hypopharynx cancer biopsies and 95 healthy tissues. The median age of the general population was 36.5 years [12, 73];the median age of the population with hypopharyngeal cancer of 40 years. Of the general study population 24.36% (38/156) was infected with HPV. In populations with hypopharyngeal cancer, HPV prevalence was 19.67% (12/61), 17.84% (5/28) in men and 21.21% (7/33) in women. HPV6 was the most frequently encountered genotype in the cancer population. Multiple infections have also been noted in cancer patients: HPV6+HPV18, HPV6+HPV56. For patients without hypopharyngeal cancer, the HPV prevalence was 27.36% (26/95), 9.59% (7/73) in women and 89.36% (19/22) in men. Several types of HPV-HR genotypes (HPV18, HPV26, HPV69), and HPV-LR genotypes (HPV42, HPV43, HPV70, HPV6) have been detected in healthy patients but also cases of co-infections (HPV6+HPV69;HPV56+HPV44;HPV58+HPV18). Conclusion: Our results showed a higher prevalence of HPV in non-cancer patients compared to hypopharyngeal cancer patients. The genotypes (HPV 6, 18 and 56) were observed in the study population. Molecular genotyping does not show a significant involvement of HPV in hypopharyngeal cancer.

Relationship between Circulating Plasma Galectin-3 Levels and T-Cell Activation during Cervical Cancer Chemotherapy

Objective: Despite the existence of several therapeutic strategies, the management of cervical cancer remains challenging. Our region has very little data on the interaction between the immune system and the clinical response to chemotherapy. This work examines plasma levels of galectin-3 (Gal-3) and percentages of activated T cells in patients with cervical cancer treated with chemotherapy and investigates if there is a relationship between the rates of these two elements. Methods: We compared data from 37 patients with cervical cancer undergoing chemotherapy and 42 controls with normal cervical cytology. Plasma Gal-3 concentrations were assessed by ELISA and expression of activation markers by T cells (CD69 and HLA-DR) was assessed by flow cytometry at three different time points during chemotherapy. Results: Our results showed that patients had a significantly higher concentration of Gal-3 compared to controls (4.025 vs. 1.340, p 0.001), similarly, they had a significantly high percentage of activated lymphocytes (2.610 vs. 0.731;p 0.0001). According to the response to treatment, patients with no response to treatment had a lower concentration of circulating Gal-3 but had approximately the same percentage of activated CD4 and CD8 lymphocytes as patients with a partial or total response. In addition, we found a positive correlation between the Gal-3 level and CD4 T cells expressing the activation marker CD69 (p 0.05;rho = 0.44). Conclusion: In conclusion, our results show that there would be a relationship between circulating galectin-3 and the percentage of peripheral CD4+CD69+ cells in cervical cancer.

Impact of COVID-19 on Biological Diagnosis of Malaria: Case of the Thierno Mouhamadoul Mansour Barro Hospital in Mbour, Senegal

Background: In Africa, malaria-endemic regions have not been spared from COVID-19 outbreak which emerged in the first quarter of 2020. This pandemic has shown clinical and therapeutic similarities with malaria. This following study sought to determine the impact of COVID-19 on the malaria diagnosis. Method: A review of laboratory registers and an exploitation of the District Health Information Software 2 (DHIS2) to collect information on the diagnosis of malaria by microscopy and by rapid diagnostic test (RDT), but also that of COVID-19 was done from 2017 to 2021 at the Thierno Mouhamadoul Mansour Hospital in Mbour, Senegal. Results: In 2017, 199 Thick drops (TDs) and 1852 RDTs were performed for malaria diagnosis. In 2018, it was 2352 malaria tests with 2138 RDTs and 214 TDs, before reaching a peak of 3943 tests in 2019 including 3742 RDTs and 201 TDs. By 2020, 2263 tests were performed with 2097 malaria RDTs, 158 TDs and 8 COVID RDTs. The latter increased significantly in 2021, reaching 444 COVID RDTs, while TDs and malaria RDT kept decreasing to 147 and 1036 respectively. Positive TDs were higher in 2020 (11.4%) compared to 2017 (3.5%), 2018 (1.4%), 2019 (6.5%) and 2021 (6.8%). For malaria RDTs, a decrease in the number of positive tests was noted between 2017 (4.5%) and 2021 (1.3%). The COVID RDTs were all negative in 2020, 29.5% were positive and 4.1% were undetermined in 2021. Conclusion: COVID-19 has led to changes in efforts to diagnose malaria as well as an increase in malaria prevalence directed towards children under 5 years of age.

Prevalence and Risk Factors of Vaginal Trichomoniasis in Women: Study at the University Hospital of Pikine in the Suburbs of Dakar, Senegal

Introduction: This study aimed to investigate the epidemiology of genital trichomoniasis in Senegal. It sought to determine the prevalence and risk factors associated with this condition in Senegal. Methodology: The study took place at the university hospital of Pikine in the suburbs of Dakar. For each of the women recruited, socio-demographic data, clinical examination data and the results of direct examination of the vaginal sample were collected in a questionnaire designed for this purpose. Results: A total of 312 women with a mean age of 31.13 (±8.41) years were recruited in this study. The majority of these women (59.94%;95% CI = 54.25 - 65.38), were seen for an infectious diseases assessment. Leucorrhea (58.33%;95% CI = 52.63 - 63.83) and genital discharge on vaginal touch (99.36%;95% CI = 97.45 - 99.89) were the predominant signs on clinical examination. The overall prevalence of vaginal trichomoniasis after direct examination of the specimens was 1.28% (95% CI = 0.41 - 3.47). Only the distribution of this prevalence by occupation was statistically significant (p = 0.0004). Conclusion: The low prevalence of genital trichomoniasis in women and the risk factors associated with it found in this study, which took place about ten years ago, should prompt an update of the data to better define the problem in Senegal.

Study of the Frequency of Superficial Candidiasis at the Fann National Hospital: Search for Candida auris

Background: Superficial candidiasis is a very frequent opportunistic disease caused by yeasts of the genus Candida. Among Candida types, some, such as Candida auris, have developed resistance to several antifungal agents. The objective of this study was to determine the hospital frequency of superficial candidiasis diagnosed at the CHU Fann and to investigate the presence of C. auris among the identified Candida strains. Methods: A cross-sectional study was conducted from February to June 2019. It involved all patients received at the Parasitology-Mycology laboratory of the CHU of Fann for suspected superficial candidiasis. Nails, skin, and vaginal specimens were subjected to direct examination and culture to identify yeasts of the genus Candida. The Candida strains were then tested by molecular biology targeting the specific C. auris ITS2 region. Results: A total of 1196 patients were examined. One thousand two hundred and five specimens (1205) were collected, including 1042 vaginal specimens, 92 nail specimens, and 71 skin specimens. Superficial candidiasis was diagnosed in 408 patients (37%). Women (34.52%) and patients under 30 years of age (39.60%) were the most affected. Yeasts of the genus Candida were found in 411 specimens (349 vaginal swabs, 36 nail fragments, and 26 skin flakes) by routine mycological techniques. The Candida albicans complex (C. albicans, C. dubliniensis, and C. africana) represented 75.91% of the Candida strains isolated. Molecular biology did not identify C. auris. Conclusion: Superficial candidiasis remains very common in hospitals in Senegal. Candida auris was not found in our study. Due to its rapid spread, surveillance is necessary to prevent epidemics in our hospitals.

Molecular Genotyping of Human Papillomaviruses (HPV) in HIV+ and HIV−Women in Senegal

Background: Different studies have demonstrated high prevalence of HPV infection and dysplastic lesions of the cervix in immunocompromised patient such as women living with HIV. Is this high prevalence due to a greater susceptibility to HPV infection, which is known to be frequent in its latent form in women? Objective: This study aims to identify HPV genotypes in HIV+ and HIV−women to understand HPV molecular epidemiology in Senegal. Material and Method: Endocervical samples from 331 HIV+ and HIV−women, sexually active, were collected. The molecular identification of the 28 genotypes studied (19 HPV-HR and 9 HPV-LR) was carried out after DNA extraction, by multiplex PCR with the Anyplex™II HPV28 detection kit from Seegene on CFX96™Bio-Rad machine. The comparisons were made by calculating the p-value and odds ratio with R Studio software (version 4.1.0). The results were considered significant if p Results: The general prevalence of HPV was significantly higher in HIV+ women with 78.95% vs 64.65% for HPV;72.18% vs 57.07% for HPV-HR;57.14% vs 34.34% for HPV-BR (p −women. Conclusion: Our results showed that the prevalence of HPV, HPV-HR and HPV-BR was significantly higher in HIV+ women. Non-vaccine genotypes were among the most found genotypes. Groups of HIV+ women aged between 35 and 50, married and using contraception were significantly more infected with HPV than the same groups of HIV-women.

Prevalence of Intestinal Parasitic Infection among Pre-School and School-Aged Children Attending to Fann University Hospital, Dakar: Results from Retrospective Analysis

Background: Intestinal parasitic infections represent a major public health problem worldwide. Pre-school and school children have a high risk of infection. The study aimed to determine the epidemiological aspects of intestinal parasitic infections in preschool and school-aged children in Dakar, Senegal. Methods: A retrospective analysis of laboratory records from preschool and school-aged children referred to the Laboratory of Parasitology at the Fann University Hospital in Dakar, Senegal, was carried out. The analysis of the period from 2016 to 2020. Stool samples were examined for the presence of parasites using direct, formal-ether concentration method and the Modified Ziehl Neelsen staining technique. Descriptive and analytic analysis was performed with Stata MP 16.1 software. Results: The overall prevalence of intestinal parasitic infection was 26.8% (429/1603). Blastocystis sp. (34%), Entamaeba coli (28%), Giardia intestinalis (9.6%), Endolimax nana (4.9%) and Ascaris lumbricoides (3.5%) were the common parasites found. Out of the 429 children positive for intestinal parasites, protozoa parasites represent 93.9%. Single infection and mixed infection represent 83.7% and 16.3%. The most prevalent associations were E. coli + Blastocystis sp. (6.3%), E. coli + E. nana (3.3%), and G. intestinalis + Blastocystis sp. (1.9%). Children between the ages of 5 - 10 years and those over 10 years had the most parasitic infections with 28.1% [aOR = 1.91;95% CI (1.25 - 2.89)] and 27.4% [aOR = 11.92 (1.07 - 3.07)]. According to the year of sample collection, the prevalence was higher in 2017, 32.6% [aOR = 1.49 (1.11 - 2.01]. The prevalence of intestinal parasitic infection was not significantly related to gender (p = 0.87), season (p = 0.85) and symptomatology (p = 0.19). The main clinical symptoms were dysenteric syndrome, dyspeptic disorders, constipation and abdominal pain. Intestinal parasite carriage in patients with acute diarrhea was 20.4%. In HIV positive with chronic diarrhea, the prevalence was 28.6%. Conclusion: The results showed the frequency of intestinal parasites in preschool and school-aged children with a high proportion of protozoa parasites. Children aged over 5 years were more affected. Preventive measures such as health education, improved socio-economic conditions and environmental sanitation are required for reducing their frequency.

Profile of Plasma Galectin-3 Concentrations, Inflammatory Cytokines Levels and Lymphocytes Status in Breast Cancer under Chemotherapy

We investigated relationship between galectin-3 (Gal-3) levels and T lymphocytes apoptosis and the activation rates in breast cancer during chemotherapy. We used plasma samples from 112 women classified into two groups: 70 women with breast cancer (BC) and submitted to neoadjuvant chemotherapy (3 cycles) and 42 healthy women used as controls. In the group of BC, blood samples were taken before each cycle of chemotherapy and Gal-3 levels was evaluated by ELISA sandwich. Flow cytometry was used to study T cells apoptosis and activation. Before treatment, median value of Gal-3 was 6.31 ng/ml (range 1.07 - 50.74) in BC and 0.84 ng/ml (range 0.00 - 4.82) in HC. Gal-3 levels were highest in plasmas from BC (p p p = 0.010). In addition, we found a dynamic relationship between gal-3 levels, tumor size and T lymphocytes apoptosis rates during treatment depending to the cure efficiency. We suggest gal-3 plasma concentrations could be used as predictive biomarker for chemotherapy efficiency in breast cancer patients.

Assessment of HRP2-Based RDT in Diagnosing Malaria Cases

Background： HRP2-based Rapid Diagnostic Tests （RDTs） for malaria ensure a rational use of artemisinin-based combination therapy （ACT）. The HRP2 antigen can go through the cerebrospinal fluid （CSF）. Purpose： To assess the HRP2-based RDT in malaria and detect the HRP2 in CSF. Methods： From November 2006 to May 2007, all patients under 15 years showing clinical symptoms of malaria were included. RDT was performed on the CSF and peripheral blood. Results： Out of the 951 patients included, 131 （13.7%） were confirmed through RDT and 130 （13.6%） through thick blood smear. Sensitivity and specificity stood at 96.96% and 99.71% respectively, for uncomplicated cases and at 100% and 99.13% for severe cases. Tests to detect HRP2 in the CSF of 52 cases were negative. Conclusion： Tests to detect HRP2 in the CSF could make it possible to diagnose severe malaria cases when peripheral parasitemia would be below the detection threshold.

Characteristics of the Heart of School-Age Children in a Schistosomiasis Endemic Area in Senegal

Introduction: In Senegal, surveys have revealed areas of high endemicity of?Schistosomiasis including the town of Richard Toll. We undertook this study?to determine the echocardiocardiographic characteristics of school-agechildren in endemic bilharziasis. Methodology: We performed a descriptive cross-sectional study in Richard Toll and Dakar in school-age children. Results: A total of 250 children were included. There was male?predominance, age between 4 and 16 (10 years old ± 2.77). Hematuria was reported in 69.6% of cases in endemic areas. Positive testing for Schistoma hæmatobium was found exclusively in Richard-Toll at 33.5%. The diastolic, systolic, basal and median left ventricle dimensions were larger in Richard Toll’s population compared to Dakar. It was the same for the right chambers dimensions. The average pulmonary systolic arterial pressure was greater in Richard-Toll: 26.38 ± 3.16 mmHg versus 21.82 ± 1.73 mmHg in Dakar (p Conclusion: The heart of the school-aged child in endemic area is characterized by larger cavitary dimensions.

Modeling a Local Geoid: Application in Thies, Senegal

Many applications in geodesy, hydrography and engineering require determining heights linked to the geoid. Direct leveling, which is the traditional method of obtaining these elevations, is slow, time consuming and expensive. The contribution of space techniques can make it possible to overcome these constraints provided that we have a precision geoid model compatible with that obtained by the GNSS method. There are today relatively precise regional geoid models, at least outside of mountain ranges, in all developed countries, which is not yet the case in developing countries like Senegal. An alternative is to use local models restricted to a small area. Thus, this study aims to produce a geoid model by combining multi-source data for the city of Thies intended mainly to support leveling operations by GNSS. To achieve this objective, direct precision leveling and GNSS leveling (static mode) were carried out covering the study area. The reference points used are, among others, those of the RRS04 (Reference Network of Senegal 2004) and the NGAO53 (General Leveling of West Africa 1953). Additionally, gravimetric measurements were conducted using the Sensor Play-Data Recorder application. The calculation of the model was carried out by the SRBF (Spherical Radial Basis Function) method using the PAGravf4.5 software. The SRBF method uses EGM08 to first calculate height and gravity anomalies. These are then compared with the raw data in order to determine the residuals which will allow the model to be refined. In order to validate our model, control points (GNSS/leveled) were chosen based on a homogeneous geographical distribution in the area in order to evaluate their altitude. An accuracy of less than 2 cm was obtained. Comparing our model with the existing local model GGSV12v1 shows that our model is more accurate.

Schistosomiasis control in Senegal:results from community data analysis for optimizing preventive chemotherapy intervention with praziquantel

Background Over the past two decades,preventive chemotherapy(PC)with praziquantel(PZQ)is the major strategy for controlling schistosomiasis in Senegal.The objective of this analysis was to update the endemicity of schistosomiasis at community level for better targeting mass treatment with PZQ in Senegal.Methods Demographic and epidemiological data from 1610 community health areas were analyzed using the schistosomiasis community data analysis tool of Expanded Special Project for Elimination of Neglected Tropical Diseases which developed by World Health Organization/Africa Ofce(WHO/AFRO).The tool uses a WHO/AFRO decision tree for areas without epidemiological data to determine whether mass treatment should be continued at community level.Descriptive analysis was performed.Results Overall,the endemicity of 1610 community health areas were updated based on the data from the district endemicity(33.5%)and the form of Join request for selected PC medicine(40.5%).Up to 282(17.5%)and 398(24.7%)of community health areas were classifed as moderate and high endemicity.41.1%of communities were non endemic.High endemicity was more important in Tambacounda,Saint Louis,Matam,Louga and Kedougou.A change in endemicity category was observed when data was disagregted from district level to community level.Implementation units classifed non endemic were more important at community level(n=666)compared to district level(n=324).Among 540 areas previously classifed high endemic at district level,392(72.6%)remained high prevalence category,while 92(17.0%)became moderate,43(8.0%)low and 13(2.4%)non-endemics at community level.Number of implementation units requiring PC was more important at district level(1286)compared to community level(944).Number of school aged children requiring treatment was also more important at district level compared to community level.Conclusions The analysis to disaggregate data from district level to community level using the WHO/AFRO schistosomiasis sub-district data optimization tool provide an update of schistosomiasis endemicity at community level.This study has allowed to better target schistosomiasis interventions,optimize use of available PZQ and exposed data gaps.