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

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 mireille sylvie kouamé-sina Zeinab Ouattara David Ngolo Coulibaly Brice Kouakou Bla mireille 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

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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（美国分子生物学期刊） 2024年第3期 166页

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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 mireille Sylla Aboubacar Tossea Koui Stéphane Kouakou Venance Adagba Marius Apia N’Chouo kouamé Basile Touré Offianan André Dosso mireille 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

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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（美国分子生物学期刊） 2024年第3期 138页

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Team experience of nasopharyngeal samples reception,decontamination,and sorting during the COVID-19 pandemic(2020)at Institut Pasteur Côte d’Ivoire

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Journal of Biosafety and Biosecurity 2021年第2期3卷 120-124页

作者： kouaméInnocent Kolia KipréBertin Guédé Kan Stéphane Kouassi Koby Albert Obro Kpadraux Danielle Odegue sylvie Mireil sina-kouaméle Banga Victor Yepri mireille Dosso Molecular Biology Platform/Institut Pasteur Côte d’Ivoire Central Laboratory/University Hospital Center of Yopougon(Côte d’Ivoire)Cote d’Ivoire Bacteriology and Virology Department National Reference Center for Antibiotics/Institut Pasteur Côte d’IvoireCôte d’Ivoire Molecular Biology Platform/Institut Pasteur Côte d’Ivoire Côte d’Ivoire Cell Biology Unit/Institut Pasteur Côte d’Ivoire Côte d’Ivoire Transport and packaging unit/Institut Pasteur Côte d’Ivoire Côte d’Ivoire Institut Pasteur Côte d’Ivoire Côte d’Ivoire

Molecular testing sensitivity,which allows for early diagnosis of the 2019 coronavirus disease(COVID-19),could be affected by sample quality,storage,and transportation timeframe to the laboratory,along with bias related to the pre-analytic *** present study reports the selection and decontamination of nasopharyngeal samples during COVID-19 management at the Institut Pasteur Côte d’*** objective of this work was to organize sample reception management and report a complete picture of sample selection and decontamination in the context of diagnosis activity *** administrative note creating the selection and decontamination unit of nasopharyngeal samples initiated activities in May *** required human resources and necessary materials were identified and put in *** activity consisted of receiving,sorting,decontaminating,and sending nasopharyngeal samples to different diagnostic *** were recorded *** a six-month period of activities,from a total amount of 11,401 containers received and decontaminated,174,085 samples were selected.A proportion of 92.0%of these specimens met the diagnostic standards,while 7.0%that were found acceptable showed minor ***,a rate of 1.0%of samples with major abnormalities could not be used for COVID-19 testing and,therefore,were ***,the non-conformity rate was reduced by 2.4%after the first term *** and decontamination of nasopharyngeal samples are crucial steps in biosafety optimization for the technical staff and quality improvement of sample care.

关键词： Sorting and decontamination Nasopharyngeal sample COVID-19 Côte d’Ivoire

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