SARS-CoV-2 shedding dynamics and transmission in immunosuppressed patients

Figures & data

Table 1. Clinical samples and SARS-CoV-2 rRT-PCR assay in this study.

Patient	ID	Collection date	Day	Sample type	rRT-PCR (Ct, E/RdRP)
Patient 1	1-S1	03-Sep-2020	1	Sputum	12.92/14.97
	1-S2	03-Sep-2020	1	Nasopharyngeal swab	14.88/17.03
	1-S3	17-Sep-2020	15	Sputum	16.6/18.32
	1-S5	24-Sep-2020	22	Sputum	17.03/18.32
	1-S6	24-Sep-2020	22	Nasopharyngeal swab	17.88/19.37
	1-S7	12-Oct-2020	40	Nasopharyngeal swab	16.14/17.3
	1-S8	25-Oct-2020	53	Sputum	22.07/23.46
	1-S9	25-Oct-2020	53	Nasopharyngeal swab	16.41/17.06
	1-S12	12-Nov-2020	71	Sputum	20.12/21.26
	1-S17	05-Feb-2021	156	Sputum	26.21/26.04
Patient 2	2-S1	20-Nov-2020	0	Nasopharyngeal swab	12.22/11.55
	2-S2	02-Dec-2020	12	Nasopharyngeal swab	16.51/15.86
	2-R1	02-Dec-2020	12	Saliva	27.93/28.27
	2-S4	02-Dec-2020	12	Stool	24.83/25.17
	2-R4	07-Dec-2020	17	throat swab	18.93/18.23
	2-S6	09-Dec-2020	19	Nasopharyngeal swab	16.67/16.92
	2-S7	09-Dec-2020	19	Saliva	21.15/21.15
	2-S8	09-Dec-2020	19	Stool	20.64/21.83
	2-R2	09-Dec-2020	19	Urine	30.19/30.62
	2-S10	19-Dec-2020	29	Nasopharyngeal swab	20.05/19.24
	2-S11	28-Dec-2020	38	Nasopharyngeal swab	14.76/14.47
	2-S12	11-Jan-2021	52	Nasopharyngeal swab	21.55/20.44
	2-R8	13-Jan-2021	54	Saliva	24.05/24.09
	2-R10	18-Jan-2021	59	Nasopharyngeal swab	25.91/25.23
	2-R11	22-Jan-2021	63	Nasopharyngeal swab	23.96/23.75
	2-R12	26-Jan-2021	67	Nasopharyngeal swab	25.23/24.65
Patient 2’ mother	2-R3	11-Jan-2021		Nasopharyngeal swab	20.56/26.74

Day 0 was the day of clinical diagnosis. Cycle threshold (Ct) values <40 were defined as positive. Ct, Cycle threshold; rRT-PCR, real-time reverse-transcription PCR.

Figure 1. Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 strains. A maximum likelihood phylogenetic tree was generated with 27 sequences from this study (yellow, n = 26; green, n = 1) and 149 SARS-CoV-2 genomes obtained from GISAID. All of the SARS-CoV-2 genomes in South Korea were downloaded from the GISAID database, and 149 sequences that matched the proportion of sequences and date range of sample collection as the total dataset were obtained. Diamond and triangle at each branch tip represent samples from patient 1 and patient 2, respectively.

Figure 2. Heatmap representing SARS-CoV-2 variant allele frequency of each variant detected in the samples. Variants that were not detected because of low coverage are shown in black.

Figure 3. Pairwise genetic distance among serial SARS-CoV-2 respiratory samples during the course of infection. The L1 norm genetic distances are shown by a colour gradient and size difference. Sputum specimens (patient 1) and nasopharyngeal swabs (patient 2) for each time point were analysed.

Figure 4. Temporal dynamics of SARS-CoV-2 variants within spike gene and corresponding viral loads during the patient’s course of infection in each patient (A and C, patient 1; B and D, patient 2). A lower cycle threshold (Ct) value corresponds to a higher viral load.

Figure 5. Genetic distance between sample pairs. (a) Sample pairs were classified into three subgroups: (1) intrahost sample pairs obtained at different time points, (2) intrahost sample pairs obtained from different anatomic sites. (b) the sample pairs were categorized into urine/non-urine sample pairs and non-urine/non-urine sample pairs. Box (median ± 25%) and whisker (5% and 95%) plots represent the distribution of the genetic distances (L1 norm) between sample pairs.

Data availability statement

Data obtained in this study were submitted to the Sequence Read Archive (SRA) (https://doi.org/10.1080/21505594.2022.2101198) under accession PRJNA801401.