Coding-Complete Genome Sequences of a Delta Subvariant (AY.33) of SARS-CoV-2 Obtained from Moroccan COVID-19 Patients

Rashid

Eur J Clin Investigation

et al. 2023

BackgroundThe pandemic of coronavirus disease 2019 (COVID‐19) has a broad spectrum of clinical manifestations. The severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) undergoes continuous evolution, resulting in the emergence of several variants. Each variant has a different severity and mortality rate.Materials and MethodsIn this study, 1174 COVID‐19 patients were studied for mortality and severity over three SARS‐CoV‐2 predominating variant periods in 2021 and 2022 in Sulaimani Province, Iraq. In each period, a representative, variant virus was subjected to phylogenetic and molecular and clinical analysis.ResultsPhylogenetic analysis revealed three SARS‐CoV‐2 variants, belonging to: Delta B.1.617.2, Omicron BA.1.17.2, and Omicron BA.5.6. The Delta variants showed more severe symptoms and a lower PCR‐Ct value than Omicron variants regardless of gender, and only 4.3% of the cases were asymptomatic. The mortality rate was lower with Omicron (.5% for BA.5.2 and 1.3% for BA.1.17.2) compared with Delta variants (2.5%). The higher mortality rate with Delta variants was in males (2.84%), while that with Omicron BA1.17.2 and BA.5.2 was in females, 1.05% and .0%, respectively. Age group (≥70) years had the highest mortality rate; however, it was (.0%) in the age group (30–49) years with Omicron variants, compared with (.96%) in Delta variants.ConclusionsThere has been a surge in COVID‐19 infection in the city due to the predominant lineages of SARS‐CoV‐2, B.1.617, Omicron BA.1.17.2 and Omicron BA.5.6, respectively. A higher PCR‐Ct value and severity of the Delta variant over Omicron BA.1.17.2 and/or BA.5.2 variants were significantly correlated with a higher death rate in the same order.

Section: Discussionsupporting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Clinical outcomes and phylogenetic analysis in reflection with three predominant clades of SARS‐CoV‐2 variants

Rashid

Eur J Clin Investigation

et al. 2023

Microbiol Resour Announc

“…Both genomes had 16 amino acid changes in the spike protein, including the S-to-F change at position 371 (S371F) and S373P in the receptor binding domain (RBD) region and L452R in the receptor binding motif (RBM) region. These mutations alter the site conformations of the S protein, resulting in reduced sensitivity to neutralizing antibodies ( 6 , 7 ), a decrease in treatment efficacy ( 8 , 9 ), and high transmissibility ( 10 ). Other protein mutations (N, E, M, and ORF1ab) were also detected with P681H in the S1/S2 furin cleavage site, which can prompt a rapid fusion between the virus and the cell membrane, resulting in increasing viral pathogenesis ( 11 , 12 ).…”

Section: Announcementmentioning

confidence: 99%

Coding-Complete Genome Sequences of an Omicron Subvariant (BA.5.2.20) of SARS-CoV-2

Rhazzar,

Hemlali,

Melloul

et al. 2023

Self Cite

“…The second most dominant lineage among SARS-COV-2 sequences was Delta variant (B.1.617.2 and AY.33) were compromised 22% of the sequenced strains (AY.33 is a sublineage of the Delta variants B.1.617.2 (Doerksen et al, 2021)). Previously, the delta variant was recorded among SARS-COV-2 sequence samples of KRG (Rashid and Salih, 2022), Morocco, England, Brazil (Hemlali et al, 2022, Smallman-Raynor and Cliff, 2022, Lima et al, 2021, and other countries (Planas et al, 2021b). The major concern about the delta variants is the ability to escape from neutralizing monoclonal and polyclonal antibodies that were produced from previous infection of the virus or by vaccination (Planas et al, 2021a).…”

Section: Sars-cov2 Variants In Kurdistanmentioning

confidence: 99%

Tracking SARS-CoV-2 variants in Kurdistan Region of Iraq.

2023

ZJPAS

SARS COV-2, the etiology of the ongoing COVID-19 pandemic, is a positive single-stranded RNA virus which was first identified in the city of Wuhan in 2019. Since its first discovery, several variants of the virus have been reported around the world. Identifying the emerged SARS-CoV-2 variants overtime is important since this could alter the pathogenicity and transmissibility of the virus as well as the efficacy of the vaccine. Here, 34 genome sequence of SARS COV-2 samples, which were collected between Feb. 2021 to Dec. 2021 in Kurdistan Region of Iraq (KRG), were compared and analyzed in the spike (S) protein region. The nucleotide sequences were collected from the GISAID database (https://gisaid.org/), and the SARS-COV-2 variants were determined based on the mutations that they carry. Additionally, the frequency of each mutation was determined in the S protein region of the isolates. Overall, 29 mutations were detected in the sequence samples; the majority (44.8%) were located in the Nterminal domain (NTD) of the protein, whereas only 10.3% located in the ribosomal binding domain (RBD). D614G was found in all sequenced strains, followed by 67.6% mutation of P681H. Moreover, seven deletions were found in the NTD of the S protein, with 61.8% of the deletions was occurred at the position Y144. Alpha variants (B.1.1.7) were found to be dominant lineage during the period of this study, accounted for 65% of the sequence samples. Overall, our data support the speedy increase of the SARS-COV-2 genome diversity. Based on our knowledge, this is the first mega sequence analyses of different SARS-COV-2 strains from KRG of Iraq.