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.