[SUGGESTION] https://doi.org/10.1101/2022.05.25.22275533 ( Gonzalez-Reiche et al) Number of case series': N = 4 case, N=15+ sequences

[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.

*Note: cases are from different indvididuals - may wish to truncate input only to samples from the index patient - aka up and including sequence EPI_ISL_11897525

*ALSO: suggest contracting submitters directly to see if there are additional sequences?

Information on case series

Accession	Day / Date	Coverage %	DOI
EPI_ISL_11178997	14/02/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275533
--------------	----------------	-----------------	---------
EPI_ISL_11179080	02/03/2022	Stretches of NNNs (3.57% of overall sequence). Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275534
EPI_ISL_11628400	16/03/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275535
EPI_ISL_11685451	10/03/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275536
EPI_ISL_11685480	14/03/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275537
EPI_ISL_11696379	17/03/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275538
EPI_ISL_11897513	20/01/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275539
EPI_ISL_11897516	06/02/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275540
EPI_ISL_11897525	19/03/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275541
EPI_ISL_12422465	08/04/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275542
EPI_ISL_12711034	21/04/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275543
EPI_ISL_12961673	18/04/2022	Stretches of NNNs (3.70% of overall sequence). Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275544
EPI_ISL_13350580	18/04/2022	Insertion of 9 nucleotides when compared to the reference WIV04 sequence. Gap of 39 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275545
EPI_ISL_13350591	07/05/2022	Gap of 36 nucleotides when compared to the reference WIV04 sequence.	https://doi.org/10.1101/2022.05.25.22275546