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PCR-HRm for Genomic Surveillance of SARS-CoV-2: A Variant Detection Tool in Côte d’Ivoire, West Africa

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American Journal of molecular Biology 2024年第3期14卷 166-185页

作者： Aboubacar Sylla Solange Kakou-Ngazoa Tata Gniré Safiatou Coulibaly Yakoura Karidja Ouattara m.reille Sylvie Kouamé-Sina Zeinab Ouattara David Ngolo Coulibaly Brice Kouakou Bla m.reille dosso molecular Biology Platform Pasteur Institute Cte dIvoire Abidjan Cte dIvoire Laboratory of Biology and Health UFR Biosciences University Flix Houphout Boigny Abidjan Cte dIvoire Genetic and Cancer Laboratory Molecular Genetics Platform Pasteur Institute Cte dIvoire Abidjan Cte dIvoire Epidemic Virus Department Pasteur Institute Cte dIvoire Abidjan Cte dIvoire

The rise of new viruses, like SARS-CoV-2 causing the COVID-19 outbreak, along with the return of antibiotic resistance in harmful bacteria, demands a swift and efficient reaction to safeguard the health and welfare of the global population. It is crucial to have effective measures for prevention, intervention, and monitoring in place to address these evolving and recurring risks, ensuring public health and international security. In countries with limited resources, utilizing recombinant mutation plasmid technology in conjunction with PCR-HRm could help differentiate the existence of novel variants. cDNA synthesis was carried out on 8 nasopharyngeal samples following viral RNA extraction. The P1 segment of the SARS-CoV-2 Spike S protein was amplified via conventional PCR. Subsequently, PCR products were ligated with the pGEm-T Easy vector to generate eight recombinant SARS-CoV-2 plasmids. Clones containing mutations were sequenced using Sanger sequencing and analyzed through PCR-HRm. The P1 segment of the S gene from SARS-CoV-2 was successfully amplified, resulting in 8 recombinant plasmids generated from the 231 bp fragment. PCR-HRm analysis of these recombinant plasmids differentiated three variations within the SARS-CoV-2 plasmid population, each displaying distinct melting temperatures. Sanger sequencing identified mutations A112C, G113T, A114G, G214T, and G216C on the P1 segment, validating the PCR-HRm findings of the variations. These mutations led to the detection of L452R or L452m and F486V protein mutations within the protein sequence of the Omicron variant of SARS-CoV-2. In summary, PCR-HRm is a vital and affordable tool for distinguishing SARS-CoV-2 variants utilizing recombinant plasmids as controls.

关键词： Genomic Surveillance SARS-CoV-2 PCR-HRm Variants Côte d’Ivoire

Dissemination of Resistance Integrons and Genes Coding for Blse and Cabapenemases in the Urban Drainage Network in Cote d’Ivoire

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Advances in microbiology 2024年第5期14卷 268-286页

作者： Coulibaly Kalpy Julien Diaby Aboubakar Sidik Vakou N’dri Sabine m’bengue Gbonon Valérie Carole Claon Jean Stephane Yao Kouamé Eric Gnali Gbohounou Fabrice Yéo Yéfougnini Bagré Issa Djaman Allico Joseph dosso m.reille Pasteur Institute of Ivory Coast Abidjan C&#244te d&#8217Ivoire Fé lix Houphou&#235t-Boigny University Abidjan C&#244te d&#8217Ivoire

Antibiotic resistance has become a major threat to human health worldwide. Environment, particularly the water environment, has long been overlooked as a player in the antibiotic resistance cycle, although its role remains unclear. These can provide an ideal setting for the acquisition and dissemination of antibiotic resistance, as they are frequently affected by anthropogenic activities. The objective of this study was to establish a diffusion map of resistance integrons used as genetic markers of resistance associated with antibiotic resistance conferring genes (ARGs). Total DNA extracts from non-cultivable bacterial communities were used for the analyses. These communities were obtained from wastewater samples from 14 sites upstream and downstream of drainage channels or effluents in the cities of Abidjan, Bouaké, and Yamoussoukro. The results obtained correspond to the number of positives among the treated samples (n = 39). Among the genetic markers of dissemination, class 1 integrons were the most evident in 94.8% of samples in Abidjan (93.3%), Bouaké (100%) and Yamoussoukro (91.6%). Class 2 integrons and class 3 integrons were found respectively in 41% and 51% of all samples. Genes coding for β-lactamases and blaTEm was identified in almost all samples at a rate of 97.4%. A co-presence of the three genes blaTEm, blaSHV and blaCTX-m is also remarkable in the sites of the city of Yamoussoukro. Among the genes coding for carbapenemases, only blaKPC 17.94%, blaNDm 30.76% and blaOXA48 38.46% were detected in the samples.

关键词： Antibiotic Resistance Wastewater Resistance Integrons (RIs) Resistance Genes

Detection of ARV-Resistant mutants in HIV-1-Infected Individuals in a Context of Systematic Switching to an Association Based on Dolutegravir in Abidjan, Côte d’Ivoire

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American Journal of molecular Biology 2024年第3期14卷 138-151页

作者： Odegue Kpadraux Danielle Kakou-Ngazoa Solange Dechi Jean-Jacques Renaud Diallo Zelica Sina Kouamé m.reille Sylla Aboubacar Tossea Koui Stéphane Kouakou Venance Adagba marius Apia N’Chouo Kouamé Basile Touré Offianan André dosso m.reille molecular Biology Platform Institut Pasteur Abidjan Cte dIvoire Laboratory of the Regional Blood Transfusion Center Yamoussoukro Cte dIvoire Department of Infectious and Tropical Diseases University Hospital Treichville Abidjan Cte dIvoire Laboratory of the Regional Blood Transfusion Center San-Pdro Cte dIvoire Department of Epidemic Virus Institut Pasteur Abidjan Cte dIvoire Department of Parasitology mycology Institut Pasteur Abidjan Cte dIvoire Department of Bacteriology-Virology Institut Pasteur Abidjan Cte dIvoire

The emergence of antiretroviral resistance mutations represents a major threat to the achievement of national and global goals for the elimination of HIV-1 infection. The global strategy in 2019 in Cte d'Ivoire is a new national policy for the management of people living with HIV with the administration of dolutegravir (DTG)-based fixed-dose combination. The aim of our study was to evaluate HIV-1 resistance to antiretrovirals (ARVs) in infected adult subjects in Cte d’Ivoire in the context of a systematic switch to a DTG-based combination. Between February 2022 and October 2023, a cross-sectional survey with random sampling was conducted in 06 services caring for people living with HIV. A total of 139 participants were included in the study. Adults with a viral load ≥ 1000 copies/mL were tested for HIV-1 ARV resistance mutations. molecular analyses were performed using protocol of ANRS-mIE (National Agency for Research on AIDS and emerging infectious diseases). The interpretation is performed by HIVGRAD (https://***/cms/grade/). The frequencies of HIV-1 resistance to non-nucleotide reverse transcriptase inhibitors (NNRTIs), nucleotide reverse transcriptase inhibitors (NRTIs), integrase inhibitors (IINTs) and protease inhibitors (PIs) were 82%, 73%, 19% and 11% respectively. The main mutations observed in the different classes were K103N (45%), m184V (64%), E157Q (19%) and L10V/m46I/A71V/I54V (6%) respectively. This study reveals the emergence of resistance to DTG-based fixed-dose combinations, favored by high rates of resistance to NRTIs and NNRTIs. This finding underlines the need for enhanced viral load monitoring and HIV-1 genotyping tests to guide the choice of NRTIs for combination therapy. In addition, monitoring for mutations to second-generation NRTIs is essential, given the scale-up of DTG-based regimens currently underway in Cte d’Ivoire.

关键词： Resistant mutants Dolutegravir HIV-1 Antiretrovirals Côte d’Ivoire

Epidemiological Facies of Human Rabies Deaths in Côte d’Ivoire from 2016 to 2022

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Open Journal of Epidemiology 2023年第4期13卷 372-384页

作者： Tiembré Issaka Tetchi Sopi malthide Coulibaly Adama Christiane Djoman Dagnan N’cho Simplice dosso m.reille Félix Houphouë t Boigny University Abidjan C&#244te d’Ivoire National Institute of Public Hygiene Abidjan C&#244te d’Ivoire National Institute of Public Hygiene Adzopé C&#244te d’Ivoire Pasteur Institute of Cô te d’Ivoire Laboratory Abidjan C&#244te d’Ivoire

Introduction: Rabies is a highly fatal viral disease outside the post-exposure prophylaxis (PEP). Data from previous studies and reports from the rabies center show that cases of death from human rabies are regularly reported, despite training measures for health workers, awareness-raising and communities, and the availability of vaccines. Objectives: The aim of this study was to analyse the determinants of human rabies deaths in Côte d’Ivoire from 2016 to 2022. method: A retrospective cross-sectional qualitative study was carried out from January to August 2023 on all the records of patients who died of human rabies at the Treichville Rabies Center from 2016 to 2022. An analysis of the rabies center’s annual activity reports from 2016 to 2022 was also carried out in order to complete the information gathered from the files. Results: The socio-demographic characteristics showed that out of 148 deaths, children accounted for 47.97% (71) and 66.22% (98) of rabies deaths were male, with an m/F sex ratio of 1.96. In terms of clinical characteristics, in 97.30% (144) of cases, the deceased had presented with furious rabies, and analysis by the Pasteur Institute of Côte d’Ivoire laboratory confirmed 101 cases (92.66%) of human rabies. Geographical distribution showed that cases of human rabies were recorded in 56 health district, and 64% (94) of the deceased lived in rural areas. The main causes of the occurrence of rabies were essentially non-use of post-exposure prophylaxis (PEP) and missed vaccination due to ignorance. Conclusion: In view of these results, control strategies and interventions need to be adapted to the epidemiological characteristics of the disease, using a community-based approach with a view to eliminating dog-transmitted rabies by 2030.

关键词： Epidemiological Facies Post-Exposure Prophylaxis Rabies Deaths Côte d’Ivoire

Climate Impact on the Productivity of Sugarcane Varieties in Ferke1 Industrial Plantations

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Agricultural Sciences 2023年第7期14卷 954-976页

作者： Sinali dosso Fidèle Yoroba Benjamin Kouassi Kouakou Kouadio Adama Diawara Arsène Kobea Arona Diedhiou LAboratoire des Sciences de la matière de l’Environnement et de l’Energie Solaire (LASMES) Université Félix Houphou&#235t Boigny Abidjan C&#244te d’Ivoire Laboratoire mixte International Climat-Eau-Energy-Agriculture Université Félix Houphou&#235t Boigny Abidjan C&#244te d’Ivoire Geophysical Station of Lamto (GSL) N’Douci C&#244te d’Ivoire Université Grenoble Alpes IRD CNRS Grenoble INP IGE Grenoble France

This study assesses the climate impact on the productivity of five sugarcane varieties (R579, SP711406, m2593/92, m1400/86, and SP701006) in the industrial plantations of Ferké 1 sugar complex. It is a contribution to research efforts aimed at increasing the productivity of sugarcane varieties in the sugar fields. Also to support agricultural development and guarantee the income of planters. The sugarcane production data are from 2013 to 2017. Climatological data are measured and calculated continuously daily at the production site. In addition, the CmIP-5 (Coupled model Intercomparison Project) climate database at 1º × 1º horizontal resolution was used for the predictability of crop yields of the 5 sugarcane varieties in the near future (2021-2050) and far future (2056-2075) to improve the quality of climate services to producers. The statistical methodological approach by multiple linear regression associated with the significativity test shows important and significant coefficients of determination (R2 > 0.90) between the yields of sugarcane varieties with certain climatic parameters such as minimum and maximum temperatures, insolation, global solar radiation, and potential evapotranspiration. The impact of rainfall has not been directly evaluated because the linear models do not explicitly show sensitivities to this parameter and the total water requirements for the plot are completely assured by irrigation. The future climate projections analyzed only from extreme thermal parameters (Tmax and Tmin) highlight their strong sensitivities with yields from an idealized model. In this model, we have assumed that the water supply needed by sugarcane is always met by irrigation on different plots. moreover, linear models do not evolve fast enough in time and changes due to external environmental constraints are not too important at the plot scale. The projected thermic parameters can thus constitute a limiting factor for the

关键词： Climate Parameters Projections Yield Sugarcane Ferkessédougou

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根据非线性贝叶斯理论的界面波频散曲线反演

声学学报 2012年第3期37卷 225-231页

作者：李翠琳 Stan E dosso Hefeng Dong 中国科学院海洋研究所海洋地质与环境重点实验室青岛266071 中国海洋大学工程学院青岛266100 University of Victoria Victoria V8W 3P6 Canada Norwegian University of Science and Technology NO-7491 Trondheim Norway

通过时频分析法从海底环境噪声数据中提取界面波频散曲线,进而采用非线性贝叶斯反演方法估算海底沉积物厚度、剪切波速度、压缩波速度和密度等参数及其不确定性。参数的最大后验概率(mAP)估计值和边缘概率分布分别通过自适应单纯形模拟... 详细信息

通过时频分析法从海底环境噪声数据中提取界面波频散曲线,进而采用非线性贝叶斯反演方法估算海底沉积物厚度、剪切波速度、压缩波速度和密度等参数及其不确定性。参数的最大后验概率(mAP)估计值和边缘概率分布分别通过自适应单纯形模拟退火法和metropolis-Hastings采样法在各参数先验区间内搜索获得,采用贝叶斯信息准则(BIC)从不同参数化模型中选择最优模型。界面波频散曲线反演结果表明:满足实测数据的最优海底模型结构为3层均匀分布剪切波速度剖面结构,海底深度的反演精度在800m以内,比起压缩波速度和密度,剪切波速度的不确定性更小,对界面波频散曲线更敏感。

关键词：贝叶斯理论曲线反演面波频散非线性剪切波速度贝叶斯信息准则边缘概率分布最大后验概率

Clinical Performances of Pure TB-Lamp Kit for <i>m. tuberculosis</i>Complex Detection in Sputum Samples

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Journal of Tuberculosis Research 2017年第2期5卷 129-138页

作者： Kouassi N’guessan Jacob Adegbele Ibrahima Coulibaly Natacha Kouame-N’takpé Hortense Seck-Angu André Guei Jacquemin Kouakou m.reille dosso Laboratoire Nationale de Référence de la Tuberculose Institut Pasteur de C&ocirc te d’Ivoire Abidjan C&ocirc te d’Ivoire Centre Antituberculeux de Yopougon Abidjan C&ocirc te d’Ivoire Programme National de Lutte contre la Tuberculose Abidjan C&ocirc te d’Ivoire

Tuberculosis represents a main concern for public health worldwide. In poor countries, the most prevalent method for bacteriological confirmation re- mains Smear Sputum microscopy (SSm). This study objective was to assess clinical performances of Loop mediated Isothermal Amplification for TB detection (Lamp-TB). Sputum of patients presenting symptoms consistent with tuberculosis were collected according to the National Tuberculosis Control Programme guidelines in Centre Antituberculeux de Yopougon. SSm after Ziehl-Neelsen staining and TB-Lamp were blindly performed with spot sputum specimen. Samples, transported at Institut Pasteur de Cote d’Ivoire were decontaminated according to N-acetyl-L-cystein (NALC) method. In mycobacteria Growth Indicator Tube (mGIT), 500 μl of pellet were inoculated and incubated in mGIT 960 instrument. mPT64 antigen was detected on positive culture. Of 500 patients enrolled, 469 were included. Clinical isolates of m. tuberculosis Complex were detected for 157 (33.5%). Comparatively to culture, Sensitivity and Specificity of SSm were 86% (95% Confidence interval (CI): 81% - 91%) 96% (95%IC: 94% - 98%) respectively. TB-Lamp Sensitivity was 92% (95%CI: 88% - 96%), and Specificity 94% (95%CI: 91% - 97%). Positive Predictive Value of SSm and TB-Lamp was 91.8% and 88.8% respectively. Negative Predictive Value of TB-Lamp assay was 95.7% whereas this of SSm was 93.3%. Positive Likelihood Ratio was 15.3 for TB-Lamp and 21.5 for SSm 21.5 whereas negative Likelihood of TB-Lamp was lower than SSm. Active tuberculosis was detected in162/469 (34.5%) with TB-Lamp and 147 (31.3%) with SSm. TB-Lamp assay performances estimated from sputum samples may improve detection of active TB cases in routine.

关键词： Tuberculosis Ziehl-Neelsen TB-Lamp Assay

用接收函数得到的2012年mw7．8海达瓜伊地震附近地区的剪切波速度结构

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世界地震译丛 2016年第1期47卷 36-47页

作者： Jeremy m. Gosselin John F. Cassidy Stan E. dosso 张丽晓(译) 赵爱华(校) 不详河北省地震局邯郸中心台中国地震局地球物理研究所

2012年mw7．8海达瓜伊地震的逆冲震源机制表明该区穿过转换挤压型太平洋一北美板块边界的汇聚受俯冲作用调节，该机制对地震与海啸的灾害分析具有重要意义。本文使用5个陆基地震台的远震记录，通过接收函数非线性反演方法调查了海达瓜... 详细信息

2012年mw7．8海达瓜伊地震的逆冲震源机制表明该区穿过转换挤压型太平洋一北美板块边界的汇聚受俯冲作用调节，该机制对地震与海啸的灾害分析具有重要意义。本文使用5个陆基地震台的远震记录，通过接收函数非线性反演方法调查了海达瓜伊之下的地壳结构和俯冲范围。在2012年地震后布设了3个台站，将覆盖延伸到了东南部，这些台站在以前还没被分析过。反演估计了莫尔兹比岛很大部分的地下剪切波速度结构。结果表明存在一个深约18-26km的速度正异常，我们将其解释为浅的大陆莫霍面。我们还识别出了一个厚12～17km的剪切波低速带，其深度沿板块汇聚方向从约25km增大到42km，该层被解释为俯冲的海洋物质。这些结果首次提供了俯冲的海洋板块延伸到整个莫尔兹比岛之下的证据。

关键词：剪切波速度结构接收函数地震台非线性反演方法俯冲作用瓜板块边界海洋板块