Comparison of SARS-CoV-2 spike RNA sequences in feces and nasopharynx indicates intestinal replication

Table 2 Changes in the SARS-CoV-2 spike protein gene in the feces and the nasopharynx in patients hospitalized with COVID-19 (N = 14)

Pat-ient	Feces			NPH			Comparison feces vs NPH		Days of symptoms prior to fecal sample	Days from NPH sample to fecal sample
Pat-ient	Popula-tions (%)	Number changes majority population^a	Number changes minority population^b	Popula-tions (%)	Number changes majority population^a	Number changes minority population^b	Difference between majority populations	Difference between minority populations	Days of symptoms prior to fecal sample	Days from NPH sample to fecal sample
1	81/19	2	6	92/8	2	1	0	5	8	2
2	91/9	1	5	90/10	1	1^c	0	6	11	1
4	94/6	0	3^c	100	0		0	x	15	4
5	100	0		100	0		0		9	1
6	100	0		100	0		0		5	4
7	94/6	0	1	100	0		0	x	9	−3
8	83/17	1^c	9	91/9	0	1^c	1	10	8	0
9	95/5	1	1	100	1		0	x	17	4
10	100	1		89/11	1	1	0	y	7	0
11	94/6	1	1	91/9	1	1^c	0	2	8	8
12	91/9	1^c	4	100	0		1	x	7	1
13	100	1		100	1		0		10	8
14	100	0		90/10	0	9	0	y	13	−5
15	94/6	0	2	100	0		0	x	12	−1

^aThe spike RNA sequence of the Alpha variant (GenBank accession number: MZ344997.1) is used as reference except for patient 9 where the spike RNA sequence of the Beta variant (GenBank accession number: MW598419.1) is used as a reference
^bThe majority population of each corresponding sample is used as reference
^cReversion of amino acid 69/70 deletion present
x = viral minority populations only found in fecal samples
y = viral minority populations only found in NPH samples
Patient 3 not shown as the NPH sample was not recovered

ISSN: 1757-4749