Access microbiology最新文献

{"title":"Complete sequences of pIJ101-based Streptomyces-Escherichia coli shuttle vectors.","authors":"Katelyn V Brown, S Eric Nybo","doi":"10.1099/acmi.0.000893.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000893.v3","url":null,"abstract":"<p><p>High-copy-number plasmids are indispensable tools for gene overexpression studies in prokaryotes to engineer pathways or probe phenotypes of interest. The development of genetic tools for the industrially relevant Actinobacteria is of special interest, given their utility in producing keratolytic enzymes and biologically active natural products. Within the Actinobacteria, <i>Streptomyces-Escherichia coli</i> shuttle vectors based on the SCP2* and pIJ101 incompatibility groups are widely employed for molecular cloning and gene expression studies. Here, the sequences of two commonly used pIJ101-based <i>Streptomyces-E. coli</i> shuttle vectors, pEM4 and pUWL201, were determined using next-generation sequencing. These plasmids drive the expression of heterologous genes using the constitutive <i>ermE*p</i> promoter. pEM4 was found to be 8.3 kbp long, containing a β-lactamase gene, thiostrepton resistance marker, the <i>lacZɑ</i> fragment, a ColE1 origin of replication and the <i>Streptomyces</i> pIJ101 origin of replication. pUWL201 was found to be 6.78 kbp long, containing a β-lactamase gene, thiostrepton resistance marker, the <i>lacZɑ</i> fragment, a ColE1 origin of replication and the <i>Streptomyces</i> pIJ101 origin of replication. Interestingly, the sequences for both pEM4 and pUWL201 exceed their previously reported size by 1.1 and 0.4 kbp, respectively. This report updates the literature with the corrected sequences for these shuttle vectors, ensuring their compatibility with modern synthetic biology cloning methodologies.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11498179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental sampling for the detection of capripox viruses and peste des petits ruminants virus in households and livestock markets in Plateau State, Nigeria.","authors":"Emma Brown, David Ehizibolo, Banenat B Dogonyaro, Yiltawe Wungak, Olumuyiwa Oyekan, Adeyinka Adedeji, Sandra Ijeoma, Rebecca Atai, Moses Oguche, Mark Samson, Fabrizio Rosso, Anna B Ludi, Georgina Limon, Andrew E Shaw, Claire Colenutt, Simon Gubbins","doi":"10.1099/acmi.0.000872.v3","DOIUrl":"10.1099/acmi.0.000872.v3","url":null,"abstract":"<p><p>Multiple transboundary animal diseases (TADs) circulate in Plateau State, Nigeria, where livestock keeping is common and contributes to both the physical and socio-economic well-being of a large proportion of the population. In this study, we explored the potential for environmental sampling to detect viruses causing TADs circulating in the region. Electrostatic dust cloths were used to swab areas of the environment likely to have contact with secretions and excretions from infected animals. Samples were collected monthly from five households, one transhumance site and one livestock market in two local government areas in Plateau State between March and October 2021. These were tested for the presence of peste des petits ruminants virus (PPRV) and capripox viruses using real-time PCR. Of the 458 samples collected, 2.4% (<i>n</i> = 11) were positive for PPRV RNA and 1.3 % (<i>n</i> = 6) were positive for capripox virus DNA. A capripox differentiation assay showed that these samples were positive for sheep pox virus (<i>n</i> = 2), goat pox virus (<i>n</i> = 2) and lumpy skin disease virus (<i>n</i> = 2). Our results demonstrate that environmental sampling could be used as part of TAD surveillance in the area. Environmental swabs require little technical knowledge to collect and can be used to detect multiple viruses from a single sample.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11488666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen.","authors":"","doi":"10.1099/acmi.0.000894.v3","DOIUrl":"10.1099/acmi.0.000894.v3","url":null,"abstract":"<p><p>Fluoroquinolone-resistant <i>Escherichia coli</i> sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract and neonatal infections. Humans, companion animals and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amongst fluoroquinolone-resistant clones in Australia. However, despite the growing importance of ST1193, only three complete genomes are published in the literature, none of which are from Australia. Here we expand on the available ST1193 resources with the complete genomes of five ST1193 strains sequenced using Oxford Nanopore Technologies and Illumina. Using <i>in silico</i> genotyping, we found that all strains were multi-drug resistant, including resistances to fluoroquinolones and cephalosporins. <i>In vitro</i> antibiotic susceptibility testing mostly correlated with individual genotypes. The exception was MS8320, which had additional <i>in vitro</i> resistance to piperacillin/tazobactam, ampicillin/sulbactam, cefazolin and doripenem (carbapenem). Further investigation identified seven additional copies of an IS26 transposable unit carrying a <i>bla</i> _TEM-1B beta-lactamase gene, suggesting this tandem amplification is associated with extended resistance phenotypes. Uropathogenicity factors, including three separate siderophore-encoding loci, were conserved in chromosomal and plasmid regions. Using all complete genomes, we further elucidated the recombination events surrounding the previously described K5/K1 capsular locus switch. Phenotypic confirmation of differing capsules in Australian ST1193 strains, coupled with genetic analysis revealing insertions downstream of the capsular locus, underscored the genetic distinctions between K5 and K1 capsule encoding strains. This study provides five new reference ST1193 genomes from Australia. These include the earliest complete K5-capsule ST1193 genomes on record (collected 2007), alongside our reference genome (MS10858), a clinical isolate obtained early during the ST1193 expansion and representative of the predominant K1-associated clade. These findings lay the foundations for further genomic and molecular analyses that may help understand the underlying reasons for the rapid global expansion of ST1193.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11488385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial profile of wound site infections and evaluation of risk factors for sepsis among road traffic accident patients from Apex Trauma Centre, Northern India.","authors":"Aparna Singh, Sangram Singh Patel, Chinmoy Sahu, Amit Kumar Singh, Nidhi Tejan, Gerlin Varghese, Ashima Jamwal, Pooja Singh, Malay Ghar","doi":"10.1099/acmi.0.000836.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000836.v4","url":null,"abstract":"<p><p><b>Background.</b> Among the most significant yet often ignored health issues worldwide are trauma and accidental injuries. India accounts for 11% of global deaths in road accidents, the highest in the world, according to the World Bank report. There are limited data about the bacterial contamination of road traffic accident (RTA) wounds and their antibiotic susceptibility patterns. <b>Materials and Methods.</b> This prospective study was conducted in a tertiary care centre in northern India from January 2023 to January 2024. Wound deep swabs or aspirates were collected from RTA patients with traumatic injuries at different time intervals. Gram stain and culture were performed, and positive aerobic culture was subjected to antibiotic susceptibility testing. Organism identification was done using MALDI-TOF MS and routine biochemical tests. Blood samples were also collected to rule out bloodstream infections during follow-up if the patient became febrile or showed symptoms of systemic infection. Sepsis was defined in those patients who had two or more scores in the systemic inflammatory response syndrome criteria with a positive microbiological culture. Risk factors were evaluated for sepsis on the basis of the patient's vitals, injury characteristics, procalcitonin, Glasgow Coma Scale (GCS) score, need for mechanical ventilation and complete blood count, which were obtained from the patient's admission file. <b>Results.</b> A total of 189 wound samples were collected, of which 99 (52.38%) samples showed the growth of microorganisms. The aerobic isolates included 69 (69.69%) Gram-negative bacilli, of which the majority were <i>Klebsiella pneumoniae</i>, 28 (28.28%) Gram-positive cocci, of which the majority were <i>Staphylococcus aureus</i> and 2 (2.02%) anaerobic isolates. Among the Gram-negative isolates, none of the isolates were resistant to colistin. All <i>S. aureus</i> isolates were susceptible to vancomycin, teicoplanin and levonadifloxacin. Sepsis developed in 50 (26.45 %) patients. Significant risk factors evaluated for sepsis were a raised procalcitonin level, a low GCS score, a higher injury severity score, the need for mechanical ventilation and a raised quick sequential organ failure assessment score. <b>Conclusion.</b> It is essential to ascertain the profile of microorganisms isolated from RTA wounds in order to reduce antibiotic resistance and deliver efficient treatment.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11472858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spectrum of respiratory viruses identified from SARS-CoV-2-negative human respiratory tract specimens in Watansoppeng, Indonesia.","authors":"Irfan Idris, Isra Wahid, Ungke Antonjaya, Edison Johar, Fiqry Hasan Kleib, Ida Yus Sriyani, Aghnianditya Kresno Dewantari, Oderna Daming, Mustakim Duharing, Fatmawati Sappe, Hajar Hasan, Frilasita Aisyah Yudhaputri, Din Syafruddin, Khin Saw Aye Myint","doi":"10.1099/acmi.0.000840.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000840.v3","url":null,"abstract":"<p><p>Respiratory infections account for millions of hospital admissions worldwide. The aetiology of respiratory infections can be attributed to a diverse range of pathogens including viruses, bacteria and fungi. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2)-negative specimens from Wattansoppeng city, South Sulawesi, were analysed to study the spectrum of respiratory viruses. Samples were screened for influenza virus, enterovirus, Paramyxoviridae, Nipah virus, Coronaviridae and Pneumoviridae. Of 210 specimens, 19 were positive for respiratory syncytial virus (RSV)-A, RSV-B, human parainfluenza virus type 1 (HPIV-1), HPIV-2, human rhinovirus (HRV)-A, HRV-B, HRV-C, human metapneumovirus (HMPV), influenza A virus (IAV) and coxsackievirus A6 (CV-A6). Influenza virus was of seasonal H3N2 subtype. The HMPVs were of genotypes B1 and A2a, while one RSV-A was of the ON-1 genotype. The viruses mostly affected children with unknown severity.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11469065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics analysis of the antigenic epitopes of L7/L12 protein in the B- and T-cells active against Brucella melitensis.","authors":"Jingjie Zhang, Huricha Baigued, Shana Chen, Haiyan Borigen, Tana Tana, Fu Quan, Dezhi Yang","doi":"10.1099/acmi.0.000786.v3","DOIUrl":"10.1099/acmi.0.000786.v3","url":null,"abstract":"<p><p>The objective is to analyse the physicochemical properties, spatial structure and protein-protein interactions (PPIs) of L7/L12 protein using bioinformatics methods and predict their B- and T-cell epitopes to lay a theoretical foundation for developing a novel multiepitope vaccine (MEV). The National Center for Biotechnology Information (NCBI) database was searched for the amino acid sequences of L7/L12 from <i>Brucella melitensis</i>. In addition, the online softwares, ProtParam and ProtScale, were used to predict the physicochemical properties: NetPhos3.1 and CD-search to predict the phosphorylation sites and conserved domains; SOMPA and SWISS-MODEL to predict the secondary and tertiary structures; the STRING database to analyse the PPIs; and the IEDB, ABCpred, SVMTrip and SYFPEITHI databases to predict the B- and T-cell epitopes. L7/L12 was docked to Toll-like receptor 4 (TLR4), B-cell receptor (BCR), Major histocompatibility complex I-T cell receptor (MHC I-TCR) and MHC II-TCR complexes, respectively, and the binding ability of L7/L12 to the targeted receptors was tested. L7/L12, consisting of 124 amino acids, was determined to be a stable, intracellular, hydrophilic protein containing 6 phosphorylation sites and ribosomal protein-related conserved domains. α-helices accounted for 70.16 %, β-turns for 2.42 %, extended strands for 8.87 % and irregular coils for 18.55 % of the secondary structure. The PPIs indicated that L7/L12 was involved in the constitution of ribosomes and regulating the accuracy of the translation process. Three B-cells, two cytotoxic T lymphocytes and three helper T lymphocyte epitopes were finally screened by comparing multiple databases. L7/L12 binds to TLR4, BCR, MHC I-TCR and MHC II-TCR complexes and forms stable hydrogen bonds, respectively. L7/L12, which governs the translation curate of proteins, possesses several potentially advantageous epitopes, laying a theoretical foundation for designing MEVs.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11648563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142840722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carbapenem-resistant Citrobacter amalonaticus and VRE bacteraemia in an immunocompetent patient after a urological Rezum procedure.","authors":"David Midlick, Jason Harhay, Nathan A Summers","doi":"10.1099/acmi.0.000852.v4","DOIUrl":"10.1099/acmi.0.000852.v4","url":null,"abstract":"<p><p>In this report, we discuss the case of a 62-year-old man who presented with gross haematuria, fever, and chills 1 day after undergoing a Rezum procedure and was found to have carbapenem-resistant <i>Citrobacter amalonaticus</i> and vancomycin-resistant <i>Enterococcus faecalis</i> bacteraemia. The patient was treated with daptomycin, eravacycline, and ceftalozane-tazobactam with positive results. We discuss our case and treatment of <i>C. amalonaticus</i> bacteraemia, a pathogen with limited existing literature on its incidence, presentation, and treatment.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of the Clostridioides difficile 630Δerm putative Pro-Pro endopeptidase CD1597.","authors":"Bart Claushuis, Arnoud H de Ru, Peter A van Veelen, Paul J Hensbergen, Jeroen Corver","doi":"10.1099/acmi.0.000855.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000855.v3","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> is the leading cause of antibiotic-associated infections worldwide. Within the host, <i>C. difficile</i> can transition from a sessile to a motile state by secreting PPEP-1, which releases the cells from the intestinal epithelium by cleaving adhesion proteins. PPEP-1 belongs to the group of Pro-Pro endopeptidases (PPEPs), which are characterized by their unique ability to cleave proline-proline bonds. Interestingly, another putative member of this group, CD1597, is present in <i>C. difficile</i>. Although it possesses a domain similar to other PPEPs, CD1597 displays several distinct features that suggest a markedly different role for this protein. We investigated the proteolytic activity of CD1597 by testing various potential substrates. In addition, we investigated the effect of the absence of CD1597 by generating an insertional mutant of the <i>cd1597</i> gene. Using the <i>cd1597</i> mutant, we sought to identify phenotypic changes through a series of <i>in vitro</i> experiments and quantitative proteomic analyses. Furthermore, we aimed to study the localization of this protein using a fluorogenic fusion protein. Despite its similarities to PPEP-1, CD1597 did not show proteolytic activity. In addition, the absence of CD1597 caused an increase in various sporulation proteins during the stationary phase, yet we did not observe any alterations in the sporulation frequency of the <i>cd1597</i> mutant. Furthermore, a promoter activity assay indicated a very low expression level of <i>cd1597</i> in vegetative cells, which was independent of the culture medium and growth stage. The low expression was corroborated by our comprehensive proteomic analysis of the whole cell cultures, which failed to identify CD1597. However, an analysis of purified <i>C. difficile</i> spores identified CD1597 as part of the spore proteome. Hence, we predict that the protein is involved in sporulation, although we were unable to define a precise role for CD1597 in <i>C. difficile.</i></p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Xanthomonas citri pv. eucalyptorum strain 4866-2_S43 (formerly X. axonopodis pv. eucalyptorum): the causal agent of bacterial leaf blight on eucalypts recovered in Argentina.","authors":"German Matias Traglia, Mousami Poudel, Samuel Miño, Blanca Isabel Canteros, G V Minsavage, Anuj Sharma, Erica M Goss, Jeffrey B Jones, Alberto Gochez","doi":"10.1099/acmi.0.000827.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000827.v3","url":null,"abstract":"<p><p>We report the draft genome assembly of strain 4866-2_S43 isolated from a eucalyptus lesion in Argentina and what until recently was caused by <i>Xanthomonas citri</i> pv. <i>eucalyptorum</i> (<i>Xce</i>). The genome size is 5 188 607 bp, with a G+C content of 64.66%. Comparative analysis reveals that the closest relative of strain 4866-2_S43 is <i>Xce</i> LPF 602, isolated in Brazil. Comparison of the whole genome sequences revealed an average nucleotide identity (ANI) of 99.96% between the two strains. ANIs were determined between the whole genome sequence of strain 4866-2_S43 and the genomes of all currently validated <i>Xanthomonas</i> spp. These results revealed that strain 4866-2_S43 shared >95% similarity with <i>X. citri</i> pv. <i>citri</i> and <i>X. citri</i> pv. <i>phaseoli</i>, and <95% with <i>X. euvesicatoria</i> pv. <i>alfalfae</i>, <i>X. euvesicatoria</i> pv. <i>perforans</i>, and <i>X. euvesicatoria</i> pathovars <i>euvesicatoria</i> and <i>eucalyptii</i>.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11475742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and genomic epidemiology of SARS-CoV-2 during the first 3 years of the pandemic in Morocco: comprehensive sequence analysis, including the unique lineage B.1.528 in Morocco.","authors":"Soulandi Djorwé, Abderrahim Malki, Néhémie Nzoyikorera, Joseph Nyandwi, Samuel Privat Zebsoubo, Kawthar Bellamine, Amale Bousfiha","doi":"10.1099/acmi.0.000853.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000853.v4","url":null,"abstract":"&lt;p&gt;&lt;p&gt;During the 3 years following the emergence of the COVID-19 pandemic, the African continent, like other regions of the world, was substantially impacted by COVID-19. In Morocco, the COVID-19 pandemic has been marked by the emergence and spread of several SARS-CoV-2 variants, leading to a substantial increase in the incidence of infections and deaths. Nevertheless, the comprehensive understanding of the genetic diversity, evolution, and epidemiology of several viral lineages remained limited in Morocco. This study sought to deepen the understanding of the genomic epidemiology of SARS-CoV-2 through a retrospective analysis. The main objective of this study was to analyse the genetic diversity of SARS-CoV-2 and identify distinct lineages, as well as assess their evolution during the pandemic in Morocco, using genomic epidemiology approaches. Furthermore, several key mutations in the functional proteins across different viral lineages were highlighted along with an analysis of the genetic relationships amongst these strains to better understand their evolutionary pathways. A total of 2274 genomic sequences of SARS-CoV-2 isolated in Morocco during the period of 2020 to 2023, were extracted from the GISAID EpiCoV database and subjected to analysis. Lineages and clades were classified according to the nomenclature of GISAID, Nextstrain, and Pangolin. The study was conducted and reported in accordance with STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines. An exhaustive analysis of 2274 genomic sequences led to the identification of 157 PANGO lineages, including notable lineages such as B.1, B.1.1, B.1.528, and B.1.177, as well as variants such as B.1.1.7, B.1.621, B.1.525, B.1.351, B.1.617.1, B.1.617.2, and its notable sublineages AY.33, AY.72, AY.112, AY.121 that evolved over time before being supplanted by Omicron in December 2021. Among the 2274 sequences analysed, Omicron and its subvariants had a prevalence of 59.5%. The most predominant clades were 21K, 21L, and 22B, which are respectively related phylogenetically to BA.1, BA.2, and BA.5. In June 2022, Morocco rapidly observed a recrudescence of cases of infection, with the emergence and concurrent coexistence of subvariants from clade 22B such as BA.5.2.20, BA.5, BA.5.1, BA.5.2.1, and BF.5, supplanting the subvariants BA.1 (clade display 21K) and BA.2 (clade display 21L), which became marginal. However, XBB (clade 22F) and its progeny such XBB.1.5(23A), XBB.1.16(23B), CH.1.1(23C), XBB.1.9(23D), XBB.2.3(23E), EG.5.1(23F), and XBB.1.5.70(23G) have evolved sporadically. Furthermore, several notable mutations, such as H69del/V70del, G142D, K417N, T478K, E484K, E484A, L452R, F486P, N501Y, Q613H, D614G, and P681H/R, have been identified. Some of these SARS-CoV-2 mutations are known to be involved in increasing transmissibility, virulence, and antibody escape. This study has identified several distinct lineages and mutations involved in the genetic diversity o","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}