Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology

Laamarti, Meriem; Chemao-Elfihri, Mohammed Walid; Kartti, Souad; Laamarti, Rokia; Allam, Loubna; Ouadghiri, Mouna; Smyej, Imane; Rahoui, Jalila; Benrahma, Houda; Diawara, Idrissa; Alouane, Tarek; Essabbar, Abdelomunim; Siah, S.; Karra, Mohammed; Hafidi, Naïma El; Jaoudi, Rachid El; Sbabou, Laïla; Nejjari, Chakib; Amzazi, Saaïd; Mentag, Rachid; Belyamani, Lahcen; Ibrahimi, Azeddine

doi:10.1128/mra.00767-20

Cited by 14 publications

(24 citation statements)

References 11 publications

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“…Their study was realized by performing MAFFT multi-alignment of all retrieved genomes from GISAID and phylogeny analysis of the aligned sequences created by maximum likelihood using IQTREE. The evolutionary analysis revealed 3 clades: 20A, 20B and 20C, and authenticates the findings of [40] , which used similar methodology to investigate the phylogenesis of 250 SARS-CoV-2 genome sequences from GISAID. Sixteen variants were detected in 6 Moroccan SARS-CoV-2 genome sequences.…”

Section: Sars-cov-2 Genome Analysis Of African Isolatessupporting

confidence: 76%

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

Ekpenyong¹,

Uzoka²,

Edoho³

et al. 2020

Preprint

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BackgroundThe increased number of accessible genomes has prompted large-scale comparative studies for decerning evolutionary knowledge of infectious diseases, but challenges such as non-availability of close reference sequence(s), incompletely assembled or large number of genomes, preclude real time multiple sequence alignment and sub-strain(s) discovery. This paper introduces a cooperatively inspired open-source framework, for intelligent mining of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes. We situate this study within the African context, to drive advancement on state-of-the-art, towards intelligent infectious disease characterization and prediction. The outcome is an enriched Knowledge Base, sufficient to provide deep understanding of the viral sub-strains’ identification problem. We also open investigation by gender, which to the best of our knowledge has been ignored in related research. Data for the study came from the Global Initiative on Sharing All Influenza Data database (https://gisaid.org) and processed for precise discovery of viral sub-strains transmission between and within African countries. To localize the transmission route(s) of each isolate excavated and provide appropriate links to similar isolate strain(s), a cognitive solution was imposed on the genome expression patterns discovered by unsupervised self-organizing map (SOM) component planes visualization. The Freidman-Nemenyi’s test was finally performed to validate our claim.ResultsEvidence of inter- and intra-genome diversity was noticed. While some isolates (or genomes) clustered differently, implying different evolutionary source (or high-diversity), others clustered closely together, indicating similar evolutionary source (or less-diversity). SOM component planes analysis revealed multiple sub-strains patterns, strongly suggesting local or intra-community and country to country transmissions. Cognitive maps of both male and female isolates revealed multiple transmission routes. Statistical results indicate significant difference between the various isolate groups at the 0.05 level of significance.ConclusionThe proposed framework offers explanations to SARS-CoV-2 diversity and provides real time identification to disease transmission routes, as well as rapid decision support for facilitating inter- and intra-country contact tracing of infected case(s). Intermediate data produced in this paper are helpful to enrich the genome datasets for intelligent characterization and prediction of COVID-19 and related pandemics, as well as the construction of intelligent device for accurate infectious disease monitoring.

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Section: Sars-cov-2 Genome Analysis Of African Isolatessupporting

confidence: 76%

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

Ekpenyong¹,

Uzoka²,

Edoho³

et al. 2020

Preprint

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“…Indeed, the SARS-CoV-2 strains circulating during the early epidemic phase in Morocco are different to those circulating in the second wave. Analysis of Moroccan SARS-CoV-2 sequences from the rst wave clustered SARS-CoV-2 strains in clades G, B11, and A2 with the presence of amino acid change at D614G, which resembles strains seen in Asia, Europe, North America, Australia, and Africa, this indicating multiple SARS-CoV-2 introductions into Morocco [11][12][13]. Similarities are also evident with European strains seen at the beginning of the pandemic, and SARS-CoV-2 strains isolated in America and Africa later in the pandemic [14].…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Infection Elicits a Greater Humoral Immune Response in the Second Wave Than the First Wave

Ezzikouri

Majidi²,

Redwane³

et al. 2021

Preprint

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PurposeSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19). One year has passed since the first COVID-19 case, and concerns have emerged regarding new variants, meaning that characterizing antibody-mediated immune response dynamics is of paramount importance. Here, we evaluated the humoral immune response against SARS-CoV-2 in subjects during the first and second waves of the pandemic in Morocco. MethodsWe assessed humoral immune response in samples from 94 seropositive individuals in the first wave (February to August 2020) and 596 seropositive individuals in the second wave (December 2020 to January 2021). Plasma samples were collected from volunteer blood donors and their levels of serum IgG to SARS-CoV-2 nucleoprotein (NP) were determined using architect SARS-CoV-2 IgG chemiluminescence microparticle immunoassay.ResultsOur results revealed an increase of humoral immunity during the second wave than first wave (3.897 ± 0.079 vs. 2.842 ± 0.153, respectively, p<0.0001). Notably, we found an age-related gradient in antibody level, with higher antibody index in subjects at 45 years old and above (p= 0.01451). However, no significant difference was found according to gender (p= 0.8629). ConclusionsOur data highlighted an important issue regarding antibody-mediated immune response against SARS-CoV-2 infection during the second wave and this issue might have arisen due to the dynamics of different strains circulating during the progress of the pandemic.

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“…A new Betacoronavirus strain of the Coronaviridae family named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease 19 (COVID-19) ( 1 – 3 ). The identification of new mutations may contribute to characterizing the virus, mapping its spread, and better understanding its biological and clinical features ( 4 , 5 ).…”

Section: Announcementmentioning

confidence: 99%

Report of SARS-CoV-2 B1.1.7 Lineage in Morocco

Ouadghiri

Aanniz

Essabbar

et al. 2021

Microbiol Resour Announc

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Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology

Cited by 14 publications

References 11 publications

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

SARS-CoV-2 Infection Elicits a Greater Humoral Immune Response in the Second Wave Than the First Wave

Report of SARS-CoV-2 B1.1.7 Lineage in Morocco

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