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  1. Article ; Online: Afro-TB dataset as a large scale genomic data of Mycobacterium tuberuclosis in Africa

    Meriem Laamarti / Yasmine El Fathi Lalaoui / Rachid Elfermi / Rachid Daoud / Achraf El Allali

    Scientific Data, Vol 10, Iss 1, Pp 1-

    2023  Volume 7

    Abstract: Abstract Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this ...

    Abstract Abstract Mycobacterium tuberculosis (MTB) is a pathogenic bacterium accountable for 10.6 million new infections with tuberculosis (TB) in 2021. The fact that the genetic sequences of M. tuberculosis vary widely provides a basis for understanding how this bacterium causes disease, how the immune system responds to it, how it has evolved over time, and how it is distributed geographically. However, despite extensive research efforts, the evolution and transmission of MTB in Africa remain poorly understood. In this study, we used 17,641 strains from 26 countries to create the first curated African Mycobacterium tuberculosis (MTB) classification and resistance dataset, containing 13,753 strains. We identified 157 mutations in 12 genes associated with resistance and additional new mutations potentially associated with resistance. The resistance profile was used to classify strains. We also performed a phylogenetic classification of each isolate and prepared the data in a format that can be used for phylogenetic and comparative analysis of tuberculosis worldwide. These genomic data will extend current information for comparative genomic studies to understand the mechanisms and evolution of MTB drug resistance.
    Keywords Science ; Q
    Subject code 572
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations

    Meriem Laamarti / Tarek Alouane / Souad Kartti / M.W. Chemao-Elfihri / Mohammed Hakmi / Abdelomunim Essabbar / Mohamed Laamart / Haitam Hlali / Loubna Allam / Naima EL Hafidi / Rachid EL Jaoudi / Imane Allali / Nabila Marchoudi / Jamal Fekkak / Houda Benrahma / Chakib Nejjari / Saaid Amzazi / Lahcen Belyamani / Azeddine Ibrahimi

    Abstract: AbstractIn late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating their spread across countries. ...

    Abstract AbstractIn late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating their spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 59 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 716 site mutations, of which 457 (64%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 39 recurrent non-synonymous mutations, including 10 hotspot mutations with a prevalence higher than 0.10 in this population and distributed in six genes of SARS-CoV-2. The distribution of these recurrent mutations on the world map revealed certain genotypes specific to the geographic location. We also found co-occurring mutations resulting in the presence of several haplotypes. Thus, evolution over time has shown a mechanism of co-accumulation and the phylogenetic analysis of this population indicated that this virus can be divided into 3 clades, including a subgroup-specific to the genomes of the United States. On the other hand, analysis of the selective pressure revealed the presence of several negatively selected residues that could be useful for considerations as therapeutic target design.We have also created an inclusive unified database (http://moroccangenomes.ma/covid/) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.
    Keywords covid19
    Publisher biorxiv
    Document type Article ; Online
    DOI 10.1101/2020.05.03.074567
    Database COVID19

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  3. Article ; Online: Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations.

    Meriem Laamarti / Tarek Alouane / Souad Kartti / M W Chemao-Elfihri / Mohammed Hakmi / Abdelomunim Essabbar / Mohamed Laamarti / Haitam Hlali / Houda Bendani / Nassma Boumajdi / Oussama Benhrif / Loubna Allam / Naima El Hafidi / Rachid El Jaoudi / Imane Allali / Nabila Marchoudi / Jamal Fekkak / Houda Benrahma / Chakib Nejjari /
    Saaid Amzazi / Lahcen Belyamani / Azeddine Ibrahimi

    PLoS ONE, Vol 15, Iss 11, p e

    2020  Volume 0240345

    Abstract: In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this ... ...

    Abstract In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes

    Tarek Alouane / Meriem Laamarti / Abdelomunim Essabbar / Mohammed Hakmi / El Mehdi Bouricha / M. W. Chemao-Elfihri / Souad Kartti / Nasma Boumajdi / Houda Bendani / Rokia Laamarti / Fatima Ghrifi / Loubna Allam / Tarik Aanniz / Mouna Ouadghiri / Naima El Hafidi / Rachid El Jaoudi / Houda Benrahma / Jalil El Attar / Rachid Mentag /
    Laila Sbabou / Chakib Nejjari / Saaid Amzazi / Lahcen Belyamani / Azeddine Ibrahimi

    Pathogens, Vol 9, Iss 829, p

    Moving Toward a Universal Vaccine for the “Confined Virus”?

    2020  Volume 829

    Abstract: The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling ... ...

    Abstract The COVID-19 pandemic has been ongoing since its onset in late November 2019 in Wuhan, China. Understanding and monitoring the genetic evolution of the virus, its geographical characteristics, and its stability are particularly important for controlling the spread of the disease and especially for the development of a universal vaccine covering all circulating strains. From this perspective, we analyzed 30,983 complete SARS-CoV-2 genomes from 79 countries located in the six continents and collected from 24 December 2019, to 13 May 2020, according to the GISAID database. Our analysis revealed the presence of 3206 variant sites, with a uniform distribution of mutation types in different geographic areas. Remarkably, a low frequency of recurrent mutations has been observed; only 169 mutations (5.27%) had a prevalence greater than 1% of genomes. Nevertheless, fourteen non-synonymous hotspot mutations (>10%) have been identified at different locations along the viral genome; eight in ORF1ab polyprotein (in nsp2, nsp3, transmembrane domain, RdRp, helicase, exonuclease, and endoribonuclease), three in nucleocapsid protein, and one in each of three proteins: Spike, ORF3a, and ORF8. Moreover, 36 non-synonymous mutations were identified in the receptor-binding domain (RBD) of the spike protein with a low prevalence (<1%) across all genomes, of which only four could potentially enhance the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These results along with intra-genomic divergence of SARS-CoV-2 could indicate that unlike the influenza virus or HIV viruses, SARS-CoV-2 has a low mutation rate which makes the development of an effective global vaccine very likely.
    Keywords COVID-19 ; SARS-CoV-2 ; genomic diversity ; divergence ; hotspot mutations ; spike protein ; Medicine ; R ; covid19
    Subject code 570
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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