![]() Sequences chosen for visualization include the index case of the Australian Delta outbreak (lacking ORF7a Δ17del), the first Australian case possessing ORF7a Δ17del during the outbreak period, an Australian sample from ∼1.5 months into the outbreak that possesses ORF7a 17del, the three USA samples (all lacking ORF7a Δ17del) that match the Australian index case, and a selection of four non-Australian samples to possess ORF7a Δ17del, some of which were collected before the Australian outbreak had begun. Visualization of a 17-nucleotide deletion in ORF7a of Delta variant SARS-CoV-2 sequences (ORF7a Δ17del), and the corresponding consequences at the peptide level. In addition, immunofluorescence analysis was performed to assess the in vitro viral growth, and the mean fluorescent intensity (MFI) staining and expression patterns of ORF7a in A.2.2-infected and Delta-ORF7a Δ17del-infected cells were compared. ![]() Further, Calu-3 (lung carcinoma cell line) cells were infected with 10 3 TCID 50 (50% tissue culture infectious dose) of A.2.2, Delta-ORF7a intact, or Delta-ORF7a Δ17del and western blot analysis was performed for cell supernatants of the infected and uninfected cells. Structural modeling and protein docking analyses were performed for ORF7a. Subsequently, genomes were discarded if they were not assigned to Delta, were duplicates, did not cover the entire ORF7a gene, and/or the collection dates were not mentioned. Each genome in the dataset was searched for ORF7a del by aligning each sequence against the Wuhan Hu-1 reference SARS-CoV-2 genome. They investigated if Delta-ORF7a Δ17del produced a detectable/functional protein, the site of ORF7a localization in infected cells and assessed ORF7aΔ 17del growth in vitro.Īll GK glade genomes (predominantly comprising Delta genomes) were downloaded from the GISAID (global initiative on sharing all influenza) database. In the present retrospective study, researchers investigated the persistence of ORF7a Δ17del for months, unlike other mutations in ORF7a that have been detected worldwide in Delta genomes. Image Credit: Dotted Yeti / Shutterstock About the study Study: Persistence of a SARS-CoV-2 variant with a frameshifting deletion for the duration of a major outbreak. Delta outbreaks occurred in Australia from June 2021 to February 2022, and whole-genome sequencing (WGS) of the causative Delta variant showed ORF7a truncation due to the presence of a 17-nucleotide (nt) frameshift-inducing deletion. SARS-CoV-2 ORF7a protein deletions (del) have been reported since the initial coronavirus disease 2019 (COVID-19) pandemic period. In a recent study posted to the medRxiv* preprint server, researchers in Australia determined whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta-ORF7a Δ17del variant has a fitness advantage over the Delta variant lacking the ORF7a Δ17del deletion (Delta-ORF7a intact) and/or the SARS-CoV-2 lineage (A.2.2). By Pooja Toshniwal Paharia Reviewed by Danielle Ellis, B.Sc.
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