Volume 28, Number 9—September 2022
Research Letter
Highly Divergent SARS-CoV-2 Alpha Variant in Chronically Infected Immunocompromised Person
, Roel H.T. Nijhuis, Nathalie Worp, Marjan Boter, Babette Weller, Babs E. Verstrepen, Corine GeurtsvanKessel, Maarten L. Corsten, Anne Russcher, and Marion Koopmans
Table
Mutations detected by WGS in an immunocompromised person chronically infected with highly divergent SARS-CoV-2 Alpha variant in the Netherlands compared with Wuhan-Hu-1 variant (GenBank accession no. NC_045512.2)*
| Collection date | GISAID (ENA) accession no. | Ct value† | ORF1ab mutations | Spike mutations | E gene mutations | N gene mutations |
|---|---|---|---|---|---|---|
| 2021 Apr 13 |
EPI_ISL_10688798 (ERS1216848) |
20.3 |
||||
| 2021 Apr 28 |
NA |
17.9 |
NS |
NS |
NS |
NS |
| 2021 May 5 |
NA |
22.3 |
NS |
NS |
NS |
NS |
| 2021 May 26 |
EPI_ISL_2887843 (ERS7202253) |
22.1 |
C5178A, G5880T, C12852T, C17555A |
NM |
NM |
NM |
| 2022 Jan 31 |
EPI_ISL_10072285 (ERS10975083) |
NA‡ |
A570T, G713T, G4232T, C5178A, G5880T, C11653T, C11665T, C12528T, A12555G, C12624T, G12761T, C12774T, C12852T, C17555A, T18340C, G20578T |
T21752A, G21987T, G22578A, C22879A, G23009T, C25282T, C25350T |
T26418C |
NM |
| 2022 Feb 3 | EPI_ISL_13133128 (ERS11204596) | 23.6 | A570T, G713T, G4232T, C5178A, G5880T, C11653T, C11665T, C12528T, A12555G, C12624T, G12761T, C12774T, C12852T, C17555A, T18340C, G20578T | T21752A, G21987T, G22578A, C22879A, G23009T, C25282T, C25350T | T26418C | NM |
*Wuhan-Hu-1 strain, GenBank accession no. NC_045512.2. Ct, cycle threshold; E, envelope; ENA, European Nucleotide Association (https://www.ebi.ac.uk/ena/browser); GISAID, https://www.gisaid.org; ORF1ab, open reading frame 1ab; N, nucleocapsid; NA, not applicable; NM, no mutations compared with the sequence from the earliest timepoint; NS, whole-genome sequencing not successful; WGS, whole-genome sequencing. †Real-time PCR as described previously was performed (4) to test for the E gene and the RNA-dependent RNA polymerase gene. The lowest Ct value is reported. ‡This specimen was tested using the Aptima SARS-CoV-2 assay (Hologic, https://www.hologic.com) using the Panther system. This system does not provide Ct values.