[SUGGESTION] https://doi.org/10.1093/ve/veac104 (Halfmann et al) Number of case series': N = 1 case, 12 sequences (note: mAb usage in timecourse)

[thomasppeacock]

A case series will only be included if it fits the inclusion criteria specified in the original paper. As well as the inclusion criteria specified within the paper only public sequences with available accessions will be included in this repository via this route.

Please confirm that each of the below criteria is met by the case series('s) suggested for inclusion:

• [x ] Are at least two SARS-CoV-2 genomes from this case series publicly available?
• [ x] Is there a time period of at least 28 days between the first genome in the series and the last?
• [ x] Is there sufficient public clinical evidence that the patient possessed a suppressed immune system during the time period covered by these genomes?
• [ x] Is there sufficient evidence that these genomes are obtained by sampling the same patient?
• [ x] Is the first genome within the case series sufficiently high (>= 95% coverage overall, 100% in spike gene) quality? Later genomes can be of lower quality but the "day 0" genome is treated as a baseline.

Information on case series

Accession	Day / Date	Coverage %	DOI
EPI_ISL_4029567	27/12/2020	Gap of 1 nucleotide(s) found at refpos 13127 (FRAMESHIFT). Gap of 13 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_831496	07/01/2021	Gap of 12 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_872778	14/01/2021	Gap of 12 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_1039839	11/02/2021	Stretches of NNNs (3.90% of overall sequence). Gap of 12 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_4052911	22/03/2021	Stretches of NNNs (1.92% of overall sequence). Gap of 12 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_2833904	29/06/2021	Stretches of NNNs (4.72% of overall sequence). Gap of 12 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_5145656	04/08/2021	Stretches of NNNs (1.21% of overall sequence). Insertion of 2 nucleotide(s) found at refpos 27883 (Frameshift confirmed by submitter). Gap of 12 nucleotides when compared to the reference WIV04 sequence. %UniqueMutations 0.07%.	https://doi.org/10.1093/ve/veac104
EPI_ISL_10549162	28/09/2021	Gap of 1 nucleotide(s) found at refpos 27877 (frameshift confirmed by the submitter). Gap of 1 nucleotide(s) at refpos 27877 was previously seen. Gap of 13 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_10549163	25/10/2021	Gap of 1 nucleotide(s) found at refpos 27877 (frameshift confirmed by the submitter). Gap of 1 nucleotide(s) at refpos 27877 was previously seen. Gap of 13 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_10549164	27/10/2021	Gap of 1 nucleotide(s) found at refpos 27877 (frameshift confirmed by the submitter). Gap of 1 nucleotide(s) at refpos 27877 was previously seen. Gap of 13 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_10549165	31/12/2021	Gap of 1 nucleotide(s) found at refpos 27877 (frameshift confirmed by the submitter). Gap of 1 nucleotide(s) at refpos 27877 was previously seen. Gap of 13 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104
EPI_ISL_10549166	04/01/2022	Gap of 1 nucleotide(s) found at refpos 27877 (frameshift confirmed by the submitter). Gap of 1 nucleotide(s) at refpos 27877 was previously seen. Gap of 13 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1093/ve/veac104