key: cord-0712479-hf7u93rz authors: Hemlali, Mouhssine; Chouati, Taha; Ghammaz, Hamza; Melloul, Marouane; Alaoui Amine, Sanaâ; Rhoulam, Safaa; Touil, Nadia; Ennibi, Khalid; Oumzil, Hicham; Mohamed, Rhajaoui; Hassan, Aguenaou; El Fahime, Elmostafa title: Coding-Complete Genome Sequences of a Delta Subvariant (AY.33) of SARS-CoV-2 Obtained from Moroccan COVID-19 Patients date: 2022-02-03 journal: Microbiol Resour Announc DOI: 10.1128/mra.01099-21 sha: 874215df18e9c31955161813d8dcb9342791b320 doc_id: 712479 cord_uid: hf7u93rz We report here the complete genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from Moroccan patients with COVID-19. The analysis of these sequences indicates that the identified strains belong to the AY.33 sublineage of the Delta variant. content of 37.9%. The quality of the sequences was monitored using the Nextclade web tool version 1.7.2 (https://clades.nextstrain.org), although the determination of the mutations was carried out using the web application Cov-GLUE (http://cov-glue.cvr.gla.ac.uk/), and the lineage and sublineage were obtained using the web application Pangolin (https://pangolin.cog-uk.io/). Both samples belonged to clade GK, sublineage AY.33 of Delta variant B1.617.2 (Delta 2). The mutations within the viral genome of sample 5858 (31 mutations) and sample 5900 (30 mutations) are summarized in Table 1 , and their localization within global SARS-CoV-2 diversity are illustrated in Fig. 1 . The genomes of both samples accumulated 4 new amino acid changes within the Spike protein (T29A, T50I, T299I, and Q613) in addition to the 10 modifications that characterize the Delta 2 variant. T487K, which results in a significant modification in the conformation of the receptor binding domain (RBD), was linked to an increase in RBD binding affinity to the cell surface S T19R T29A G142D R158G T250I T299I L452R T478K Q613H D614G P681R D950N E157-F158-T19R T29A G142D R158G T250I T299I L452R T478K Q613H D614G P681R D950N E156-F157-ORF 3a S26L S26L M I82T ORF 7a V82A T120I V82A T120I ORF 7b T40I T40I ORF 8 D119-F120-ORF 9B T60A T60A N D63G R203M G215C N377Y D63G R203M G215C N377Y angiotensin converting enzyme 2 (ACE2) receptor (3). In addition, Q613H was also reported as an amino acid modification of little-known impact; however, given its close proximity to the well-known D614G, it is possible that this amino acid change would enhance the role of the latter in terms of virus transmissibility (4, 5) . Furthermore, among amino acid modifications affecting the receptor binding motif (RBM) region, L452R is present in variants which exhibit high binding affinity to the ACE2 receptor and may also contribute to humoral immune escape (6) . Another interesting amino acid change is P681R, located between subunits S1 and S2. It has been established that the P681R change increases S1/S2 cleavage, which induces a quicker fusion between virus and cell membrane, thus facilitating viral transmissibility (7) . Finally, the N-terminal domain (NTD) (an essential binding site for antibody 4A8 [8] ) is altered through G142D. This mutation contributes to changing the structure of the NTD, resulting in the binding prevention of neutralization antibodies (NAb) to this domain (9) . The characteristic B.1.617.2 and B.1.617.3 deletions 157 to 158 can also be observed and constitute another mechanism by which the virus acquired vaccine escape abilities (10) . The emergence and spread of new variants derived from volatile organic compounds (VOCs) are a global concern, their escape from vaccination is not yet well studied, and the genomic surveillance of the genome of SARS-CoV-2 remains a primary approach to identify variants and prevent their spread. Data availability. The SARS-CoV-2 genome sequences 5858 and 5900 were deposited into the GISAID database under the identifiers EPI_ISL_6002899 and EPI_ISL_6002900, respectively, and in NCBI GenBank under the accession numbers OL375239 and OL375240, respectively. Raw reads from next-generation sequencing (NGS) are available in the BioProject database under SRA number PRJNA780922. The specific raw read library identifiers of samples 5858 and 5900 are SRX13150847 and SRX13150848, respectively. This study was supported and financed by the Hassan II Academy of Science and Technology, Morocco. The genetic sequence, origin, and diagnosis of SARS-CoV-2 The establishment of reference sequence for SARS-CoV-2 and variation analysis The hCoV-19/5858 and hCoV-19/5900 strains are situated in the Delta lineage (green) and, more specifically, in the AY.33 sublineage. SARS-CoV-2 B.1.617 Indian variants: are electrostatic potential changes responsible for a higher transmission rate SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo SARS-CoV-2 one year on: evidence for ongoing viral adaptation Infection and vaccine-induced neutralizing antibody responses to the SARS-CoV-2 B.1.617.1 variant Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 Spike protein NTD mutation G142D in SARS-CoV-2 Delta VOC lineages is associated with frequent back mutations, increased viral loads, and immune evasion 2021. B.1.617.3 SARS CoV-2 spike E156G/D157-158 mutations contribute to reduced neutralization sensitivity and increased infectivity