Genetic Diversity and Genomic Epidemiology of SARS-COV-2 in Morocco

Badaoui, Bouabid; Sadki, Khalid; Talbi, Chouhra; Tazi, Lina; Salah, D. Ben

doi:10.1101/2020.06.23.165902

Cited by 7 publications

(8 citation statements)

References 21 publications

(14 reference statements)

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“…Many other missense and synonymous mutations found in respective proteins of Bangladeshi virus populations such as ORF1ab/nsp12_P323L, NS3_Q57H, NS8_R52I, N_S194L, N_R203K, and N_G204R, which are also common worldwide [ 38 ]. The mutation NSP12_P323L plays a prominent role in protein folding and aggregation [ 39 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

et al. 2021

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Virus evolution and mutation analyses are crucial for tracing virus transmission, the potential variants, and other pathogenic determinants. Despite continuing circulation of the SARS-CoV-2, very limited studies have been conducted on genetic evolutionary analysis of the virus in Bangladesh. In this study, a total of 791 complete genome sequences of SARS-CoV-2 from Bangladesh deposited in the GISAID database during March 2020 to January 2021 were analyzed. Phylogenetic analysis revealed circulation of seven GISAID clades G, GH, GR, GRY, L, O, and S or five Nextstrain clades 20A, 20B, 20C, 19A, and 19B in the country during the study period. The GISAID clade GR or the Nextstrain clade 20B or lineage B.1.1.25 is predominant in Bangladesh and closely related to the sequences from India, USA, Canada, UK, and Italy. The GR clade or B.1.1.25 lineage is likely to be responsible for the widespread community transmission of SARS-CoV-2 in the country during the first wave of infection. Significant amino acid diversity was observed among Bangladeshi SARS-CoV-2 isolates, where a total of 1023 mutations were detected. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. The wide genomic diversity indicated multiple introductions of SARS-CoV-2 into Bangladesh through various routes. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Bangladesh.

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Section: Discussionmentioning

confidence: 99%

Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

et al. 2021

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“…Among the variants were synonymous (F924F and L4715L), nonsynonymous (D->G: D614G) and intergenic (241C->T). Jouali et al [41] corroborate the inference of [39] by comparatively studying the SARS-CoV-2 genome sequence of a mildly symptomatic Moroccan patient with other sequences from Morocco. The phylogenetic analysis of the genome was conducted using GIDSAID enabled Nextstrain tool.…”

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

confidence: 82%

“…This diversity in lineage infers the introduction of SARS-CoV-2 into Morocco from multiple routes. In [39] , the molecular analysis of SARS-CoV-2 genome sequences of 22 Moroccan isolates obtained from three laboratories in Morocco as at June 7, 2020 revealed 62 mutations. In comparison with the Wuhan reference genome and 40366 viral genome sequences retrieved from GISAID, the Moroccan genome evinced similar mutations with the Wuhan reference genome and other strains circulating globally.…”

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

confidence: 99%

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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“…This study of mutations in the SARS-CoV2 genomes of 128 COVID-19 affected Indian patients has been carried out. Various mutations over the proteins of SARS-CoV2 genomes are presented in the articles [ 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. A comprehensive list of patients with other associated details are presented in the Table 1 .…”

Section: The Studymentioning

confidence: 99%

Missense mutations in SARS-CoV2 genomes from Indian patients

Hassan¹,

Choudhury

Roy

et al. 2020

Genomics

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The genetic diversity of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) in several countries sums up to worldwide genetic diversity. In this present study, variations in terms of missense mutations among the SARS-CoV2 genomes from 128 Indian patients, as of May 2020, are accounted and thereby some key findings with some hypotheses were made. These mutations across various genes of these genomes show wide genetic variations in sequence and rapid evolution of SARS-CoV2 virus. The presence of unique mutations in the studied SARS-CoV2 genomes may led to their attenuation. Few Genes such as ORF6, ORF10 are free from any mutations in the Indian context of 339 genomes observed as of 14th July 2020. Further, E protein contains only one mutation. This may suggest that designing a therapeutic approach against ORF6, ORF10 and E genes may have a beneficial effect in controlling COVID-19 pandemic especially in India.

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Genetic Diversity and Genomic Epidemiology of SARS-COV-2 in Morocco

Cited by 7 publications

References 21 publications

Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

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

Missense mutations in SARS-CoV2 genomes from Indian patients

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