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Article: Methanobrevibacter massiliense

Pilliol, Virginie / Beye, Mamadou / Terlier, Laureline / Balmelle, Julien / Kacel, Idir / Lan, Romain / Aboudharam, Gérard / Grine, Ghiles / Terrer, Elodie

Microorganisms

2024 Volume 12, Issue 1

Abstract: Among oral microbiota methanogens, ...

Abstract	Among oral microbiota methanogens,
Language	English
Publishing date	2024-01-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms12010215
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Emergence of a second SARS-CoV-2 variant with a tremendous genetic leap from its ancestors.

Colson, Philippe / La Scola, Bernard / Beye, Mamadou / Delerce, Jérémy / Raoult, Didier / Fantini, Jacques

Journal of medical virology

2023 Volume 95, Issue 10, Page(s) e29124

Abstract: The on-going emergence of the Omicron BA.2.86 variant is one of the major events in SARS-CoV-2 genetic evolution that remain enigmatic regarding the overall virus mutation rate, together with the emergence of the initial Omicron variant, BA.1. Indeed, ... ...

Abstract	The on-going emergence of the Omicron BA.2.86 variant is one of the major events in SARS-CoV-2 genetic evolution that remain enigmatic regarding the overall virus mutation rate, together with the emergence of the initial Omicron variant, BA.1. Indeed, the genomes of the Omicron BA.2.86 lineage, an offspring of the second major Omicron subvariant, BA.2, harbor 39 additional mutations in the spike compared to this ancestor. Here we comment on the phylogeny of BA.2.86, on the positions, and frequencies in other SARS-CoV-2, of mutations in its spike, and on the structural model of this protein that concentrates most of BA.2.86 additional mutations.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Family ; Evolution, Molecular ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2023-10-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29124
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Zs.A 1320: Show issues

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Article ; Online: High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol.

Papa Mze, Nasserdine / Kacel, Idir / Beye, Mamadou / Tola, Raphael / Sarr, Mariéma / Basco, Leonardo / Bogreau, Hervé / Colson, Philippe / Fournier, Pierre-Edouard

Genes

2023 Volume 14, Issue 3

Abstract: The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study ... ...

Abstract	The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/genetics ; Whole Genome Sequencing/methods ; Gene Library ; Genome, Viral
Language	English
Publishing date	2023-03-09
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14030681
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Article: Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France

Colson, Philippe / Delerce, Jeremy / Burel, Emilie / Beye, Mamadou / Fournier, Pierre-Edouard / Levasseur, Anthony / Lagier, Jean-Christophe / Raoult, Didier

Virus genes. 2022 Feb., v. 58, no. 1

2022

Abstract: Great concerns have been raised about SARS-CoV-2 variants over the past six months. At the end of 2020, an increasing incidence of spike substitutions Q677H/P was described in the USA, which involved six independent lineages. We searched for changes to ... ...

Abstract	Great concerns have been raised about SARS-CoV-2 variants over the past six months. At the end of 2020, an increasing incidence of spike substitutions Q677H/P was described in the USA, which involved six independent lineages. We searched for changes to this amino acid in the sequence database of SARS-CoV-2 genomes obtained at the IHU Méditerranée Infection (Marseille, France) from 3634 patients sampled between February 2020 and April 2021. In seven genomes (0.2%), we found a deletion of five amino acids at spike positions 675–679 (QTQTN) including Q677, and in 76 genomes (2.3%) we found a Q677H substitution. The 83 genomes were classified in ten different Pangolin lineages. Genomes with a spike Q677 deletion were obtained from respiratory samples collected in six cases between 28 March 2020 and 12 October 2020 and in one case on 1 February 2021. The Q677H substitution was found in genomes all obtained from respiratory samples collected from 19 January 2021 and were classified in seven different lineages. Most of these genomes (41 cases) were of UK variant. Two others were classified in the B.1.160 Pangolin lineage (Marseille-4 variant) which was first detected in July 2020 in our institute but was devoid of this substitution until 19 January 2021. Also, eight genomes were classified in the A.27/Marseille-501 lineage which was first detected in our institute in January 2021 and which either harboured or did not harbour the Q677H substitution. Thus, the spike Q677H substitution should be considered as another example of convergent evolution, as it is the case of spike substitutions L18F, E484K, L452R, and N501Y which also independently appeared in various lineages.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; amino acids ; convergent evolution ; databases ; viruses ; France
Language	English
Dates of publication	2022-02
Size	p. 53-58.
Publishing place	Springer US
Document type	Article
ZDB-ID	639496-6
ISSN	1572-994X ; 0920-8569
ISSN (online)	1572-994X
ISSN	0920-8569
DOI	10.1007/s11262-021-01877-2
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Zs.A 2397: Show issues

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Article ; Online: High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol

Papa Mze, Nasserdine / Kacel, Idir / Beye, Mamadou / Tola, Raphael / Sarr, Mariéma / Basco, Leonardo / Bogreau, Hervé / Colson, Philippe / Fournier, Pierre-Edouard

Genes (Basel). 2023 Mar. 09, v. 14, no. 3

2023

Abstract	The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; evolution ; genome ; pandemic
Language	English
Dates of publication	2023-0309
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14030681
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Article ; Online: Influenza at the 2021 Grand Magal of Touba and possible spread to rural villages in South Senegal - a genomic epidemiological study.

Goumballa, Ndiaw / Diouf, Fatou Samba / Beye, Mamadou / Sambou, Masse / Bassène, Hubert / Dieng, Mamadou / Aïdara, Adama / Targa, Lorlane L E / Colson, Philippe / Gautret, Philippe / Sokhna, Cheikh

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2024 Volume 141, Page(s) 106952

Abstract: Objectives: Influenza is frequent among pilgrims participating in the Grand Magal de Touba (GMT), in Senegal, with a potential to spread to contacts when they return home.: Methods: Ill pilgrims consulting at a health care center in Mbacké city close ...

Abstract	Objectives: Influenza is frequent among pilgrims participating in the Grand Magal de Touba (GMT), in Senegal, with a potential to spread to contacts when they return home. Methods: Ill pilgrims consulting at a health care center in Mbacké city close to Touba during the 2021 GMT, pilgrims returning to Dielmo and Ndiop villages, and patients who did not travel to Touba and consulted at health care centers in these two villages in 2021 were tested for the influenza virus by polymerase chain reaction on nasopharyngeal samples. Next-generation sequencing and comparative and phylogenetic analyses of influenza A virus genomes were performed. Results: A total of 62 of 685 patients tested positive for influenza A virus, including 34 of 53 who were consulted in Mbacké in late September, six of 129 pilgrims who returned home in early October, and 20 of 42 villagers from October 3 to 29. A total of 27 genomes were obtained. Four clusters were observed based on the phylogenetic analyses, suggesting that Mbacké patients and returned pilgrims may have shared closely related viral strains with patients inhabiting the villages who did not participate in the GMT. Conclusions: Villagers in Ndiop and Dielmo may have been infected with viral strains originating from the GMT and possibly imported by pilgrims who returned from the GMT.
MeSH term(s)	Humans ; Influenza, Human/epidemiology ; Senegal/epidemiology ; Phylogeny ; Epidemiologic Studies ; Real-Time Polymerase Chain Reaction ; Genomics
Language	English
Publishing date	2024-02-07
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2024.01.019
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Article ; Online: Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania.

Deida, Jemila / Papa Mze, Nasserdine / Beye, Mamadou / Ahmed, Sidi Mohamed / El Bara, Ahmed / Bollahi, Mohamed Abdallahi / Basco, Leonardo / Ould Mohamed Salem Boukhary, Ali / Fournier, Pierre-Edouard

Genes

2024 Volume 15, Issue 3

Abstract: The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the ... ...

Abstract	The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Mauritania/epidemiology ; COVID-19 Vaccines ; Genomics ; Pandemics
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2024-03-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes15030361
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Article ; Online: Advancing access to care: An assessment of the prehospital system in Senegal.

Michalski, Kamil / Diedhiou, Moustapha / Kerachian, Matin / Grushka, Jeremy / Tendeng, Jacques Noel / Diao, Mohamed Lamine / Beye, Mamadou D / Montero Ortiz, Johana / Razek, Tarek / Deckelbaum, Dan L / Konate, Ibrahim

World journal of surgery

2024 Volume 48, Issue 5, Page(s) 1056–1065

Abstract: Background: Most low- and middle-income countries do not have a mature prehospital system limiting access to definitive care. This study sought to describe the current state of the prehospital system in Senegal and offer recommendations aimed at ... ...

Abstract	Background: Most low- and middle-income countries do not have a mature prehospital system limiting access to definitive care. This study sought to describe the current state of the prehospital system in Senegal and offer recommendations aimed at improving system capacity and population access to definitive care. Methods: Structured interviews were conducted with key informants in various regions throughout the country using qualitative and quantitative techniques. A standardized questionnaire was generated using needs assessment forms and system frameworks. Descriptive statistics were performed for quantitative data analysis, and qualitative data was consolidated and presented using ATLAS.ti. Results: Two (20%) of the studied regions, Dakar and Saint-Louis, had a mature prehospital system in place, including dispatch centers and teams of trained personnel utilizing equipped ambulances. 80% of the studied regions lacked an established prehospital system. The vast majority of the population relied on the fire department for transport to a healthcare facility. The ambulances in rural regions were not part of a formal prehospital system, were not equipped with life-support supplies, and were limited to inter-facility transfers. Conclusions: While Dakar and Saint-Louis have mature prehospital systems, the rest of the country is served by the fire department. There are significant opportunities to further strengthen the prehospital system in rural Senegal by training the fire department in basic life support and first aid, maintaining cost efficiency, and building on existing national resources. This has the potential to significantly improve access to definitive care and outcomes of emergent illness in the Senegalese community.
MeSH term(s)	Senegal ; Health Services Accessibility/organization & administration ; Humans ; Emergency Medical Services/organization & administration ; Surveys and Questionnaires
Language	English
Publishing date	2024-03-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	224043-9
ISSN	1432-2323 ; 0364-2313
ISSN (online)	1432-2323
ISSN	0364-2313
DOI	10.1002/wjs.12110
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Zs.A 1336: Show issues

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Article ; Online: Simultaneous SARS-CoV-2 Genome Sequencing of 384 Samples on an Illumina MiSeq Instrument through Protocol Optimization.

Papa Mze, Nasserdine / Beye, Mamadou / Kacel, Idir / Tola, Raphael / Basco, Leonardo / Bogreau, Hervé / Colson, Philippe / Fournier, Pierre-Edouard

Genes

2022 Volume 13, Issue 9

Abstract: In the present study, we propose a high-throughput sequencing protocol using aNextera XT Library DNA kit on an Illumina MiSeq instrument. We made major modifications to this library preparation in order to multiplex 384 samples in a single Illumina flow ... ...

Abstract	In the present study, we propose a high-throughput sequencing protocol using aNextera XT Library DNA kit on an Illumina MiSeq instrument. We made major modifications to this library preparation in order to multiplex 384 samples in a single Illumina flow cell. To validate our protocol, we compared the sequences obtained with the modified Illumina protocol to those obtained with the GridION Nanopore protocol. For the modified Illumina protocol, our results showed that 94.9% (357/376) of the sequences were interpretable, with a viral genome coverage between 50.5% and 99.9% and an average depth of 421×. For the GridION Nanopore protocol, 94.6% (356/376) of the sequences were interpretable, with a viral genome coverage between 7.0% and 98.6% and an average depth of 2123×. The modified Illumina protocol allows for gaining EUR 4744 and returning results of 384 samples in 53.5 h versus four times 55.5 h with the standard Illumina protocol. Our modified MiSeq protocol yields similar genome sequence data as the GridION Nanopore protocol and has the advantage of being able to handle four times more samples simultaneously and hence is much less expensive.
MeSH term(s)	COVID-19/genetics ; Chromosome Mapping ; DNA ; High-Throughput Nucleotide Sequencing/methods ; Humans ; SARS-CoV-2/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-09-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13091648
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Simultaneous SARS-CoV-2 Genome Sequencing of 384 Samples on an Illumina MiSeq Instrument through Protocol Optimization

Papa Mze, Nasserdine / Beye, Mamadou / Kacel, Idir / Tola, Raphael / Basco, Leonardo / Bogreau, Hervé / Colson, Philippe / Fournier, Pierre-Edouard

Genes. 2022 Sept. 14, v. 13, no. 9

2022

Abstract	In the present study, we propose a high-throughput sequencing protocol using aNextera XT Library DNA kit on an Illumina MiSeq instrument. We made major modifications to this library preparation in order to multiplex 384 samples in a single Illumina flow cell. To validate our protocol, we compared the sequences obtained with the modified Illumina protocol to those obtained with the GridION Nanopore protocol. For the modified Illumina protocol, our results showed that 94.9% (357/376) of the sequences were interpretable, with a viral genome coverage between 50.5% and 99.9% and an average depth of 421×. For the GridION Nanopore protocol, 94.6% (356/376) of the sequences were interpretable, with a viral genome coverage between 7.0% and 98.6% and an average depth of 2123×. The modified Illumina protocol allows for gaining EUR 4744 and returning results of 384 samples in 53.5 h versus four times 55.5 h with the standard Illumina protocol. Our modified MiSeq protocol yields similar genome sequence data as the GridION Nanopore protocol and has the advantage of being able to handle four times more samples simultaneously and hence is much less expensive.
Keywords	DNA ; Severe acute respiratory syndrome coronavirus 2 ; nanopores ; nucleotide sequences ; viral genome
Language	English
Dates of publication	2022-0914
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13091648
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