[SUGGESTION] https://doi.org/10.1101/2022.06.29.22276868 (Chaguza et al) Number of case series': 1 patient, 30 sequences (note: divergence into lineages within patient) #2
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.
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:
Information on case series
| Accession | Day / Date | Coverage % | DOI |
EPI_ISL_10548912 | 13/09/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548913 | 27/09/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548915 | 08/02/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548916 | 18/02/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548917 | 26/02/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548918 | 05/03/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548919 | 05/04/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548920 | 03/05/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548921 | 24/05/2021 | NS6_Y31stop results in 50.8% truncation of the protein sequence. | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10548922 | 28/06/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_10815044 | 10/02/2022 | Stretches of NNNs (1.64% of overall sequence). | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_11025821 | 23/02/2022 | Gap of 3 nucleotides when compared to the reference WIV04 sequence. | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_11503909 | 07/03/2022 | Gap of 3 nucleotides when compared to the reference WIV04 sequence. | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_2035047 | 19/04/2021 | Stretches of NNNs (1.09% of overall sequence). | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_2716246 | 01/06/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_2776212 | 14/06/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_2860316 | 21/06/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_3133023 | 12/07/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_3370176 | 25/07/2021 | Stretches of NNNs (1.17% of overall sequence). | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_4198270 | 29/08/2021 | Stretches of NNNs (1.07% of overall sequence). | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_4576991 | 08/09/2021 | Stretches of NNNs (1.01% of overall sequence). | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_5395558 | 04/10/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_5639913 | 12/10/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_5865553 | 19/10/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_7361483 | 03/11/2021 | Insertion of 1 nucleotide(s) found at refpos 8905 (FRAMESHIFT). Insertion of 1 nucleotide(s) at refpos 8905 occurred >=100 times in >=10 locations. Gap of 1 nucleotide(s) found at refpos 27271 (FRAMESHIFT). | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_7361527 | 09/11/2021 | Stretches of NNNs (4.27% of overall sequence). Gap of 1 nucleotide(s) found at refpos 27271 (FRAMESHIFT). | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_7980711 | 16/11/2021 | | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_8563217 | 27/12/2021 | Stretches of NNNs (1.24% of overall sequence). Gap of 9 nucleotides when compared to the reference WIV04 sequence. | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_8563218 | 20/12/2021 | Stretches of NNNs (3.68% of overall sequence). Gap of 9 nucleotides when compared to the reference WIV04 sequence. | https://doi.org/10.1101/2022.06.29.22276868 EPI_ISL_8563219 | 07/12/2021 | Stretches of NNNs (1.24% of overall sequence). Gap of 1 nucleotide(s) found at refpos 27271 (FRAMESHIFT). Gap of 13 nucleotides when compared to the reference WIV04 sequence. | https://doi.org/10.1101/2022.06.29.22276868