| Literature DB >> 34354952 |
Ettore Capoluongo1,2, Carmela Nardelli1,2,3, Maria Valeria Esposito2, Antonio Riccardo Buonomo4, Monica Gelzo1,2, Biagio Pinchera4, Emanuela Zappulo4, Giulio Viceconte4, Giuseppe Portella5, Mario Setaro2, Ivan Gentile4, Giuseppe Castaldo1,2.
Abstract
BACKGROUND: We report the case of a woman with non-Hodgkin lymphoma who remained positive on the molecular assay for SARS-CoV-2 for six months: she has never experienced a severe form of COVID-19 although in absence of seroconversion.Entities:
Keywords: ORF3a; SARS-CoV-2; long-term infection; non-Hodgkin lymphoma; novel variant; whole genome sequencing
Year: 2021 PMID: 34354952 PMCID: PMC8329552 DOI: 10.3389/fonc.2021.705948
Source DB: PubMed Journal: Front Oncol ISSN: 2234-943X Impact factor: 6.244
List of the 22 mutations identified in the patient’s SARS-CoV-2.
| Ref Genome | Genome position | Gene | c.DNA | Coding Consequence | Protein | Protein |
|---|---|---|---|---|---|---|
| NC_045512.2 | 241 | 5’UTR | c.1-25C>T | 5’UTR | ||
| NC_045512.2 | 445 | ORF1ab | c.180T>C | synonymous | p.(Val60=) | V60= |
| NC_045512.2 | 1513 | ORF1ab | c.1248C>T | synonymous | p.(Cys416=) | C416= |
| NC_045512.2 | 2062 | ORF1ab | c.1797C>T | synonymous | p.(Ala599=) | A599= |
| NC_045512.2 | 3037 | ORF1ab | c.2772C>T | synonymous | p.(Phe924=) | F924= |
| NC_045512.2 | 4878 | ORF1ab | c.4613C>A | Missense | p.(Thr1538Asn) | T1538N |
| NC_045512.2 | 5654 | ORF1ab | c.5389C>T | synonymous | p.(Leu1797=) | L1797= |
| NC_045512.2 | 6286 | ORF1ab | c.6021C>T | synonymous | p.(Thr2007=) | T2007= |
| NC_045512.2 | 14408 | ORF1ab | c.14144C>T | Missense | p.(Pro4715Leu) | P4715L |
| NC_045512.2 | 19117 | ORF1ab | c.18853G>T | Missense | p.(Ala6285Ser) | A6285S |
| NC_045512.2 | 21255 | ORF1ab | c.20991G>C | synonymous | p.(Ala6997=) | A6997= |
| NC_045512.2 | 22227 | S* | c.665C>T | Missense | p.(Ala222Val) | A222V |
| NC_045512.2 | 22346 | S | c.784G>T | Missense | p.(Ala262Ser) | A262S |
| NC_045512.2 | 22377 | S | c.815C>T | Missense | p.(Pro272Leu) | P272L |
| NC_045512.2 | 23403 | S | c.1841A>G | Missense | p.( | D614G |
| NC_045512.2 | 25906 | ORF3a | c.514G>T | Missense | p.(Gly172Cys) | G172C |
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| NC_045512.2 | 26801 | M | c.279C>G | synonymous | p.(Leu93=) | L93= |
| NC_045512.2 | 28560 | N | c.287G>T | Missense | p.(Gly96Val) | G96V |
| NC_045512.2 | 28932 | N* | c.659C>T | Missense | p.(Ala220Val) | A220V |
| NC_045512.2 | 29085 | N | c.812C>T | Missense | p.(Thr271Ile) | T271I |
| NC_045512.2 | 29645 | ORF10* | c.88G>T | Missense | p.(Val30Leu) | V30L |
*The present three mutations are associated to the Italian lineage B.1.177.83 (11). §c.766_769del (in bold) corresponds to a new variant never reported in the other databases (depth of coverage: 1700x).
Figure 1IGV representation of the c.766_769del affecting the ORF3a gene.
Figure 2Phylogeny of SARS-CoV-2 clade obtained in our female patient.