Table 3 Distribution of single-nucleotide variants in NoV by gene. Single nucleotide variants (SNVs) were identified using FreeBayes in two samples (SP1 and SP2) collected four months apart from an immunocompromised bone marrow transplant patient with chronic NoV infection. Only those SNVs found at frequencies ≥ 2 % and with 5X coverage are reported. Positions with coverage < 10X were excluded from the analysis
ORF | Gene (other names) | Position (nt) | SP1 | SP2 | ||
|---|---|---|---|---|---|---|
S | NS (P-value*) | S | NS (P-value*) | |||
1 | p48 (NS1-2, N-term, p37) | 1–983 | 6 | 2 (0.5) | 11 | 2 (0.8) |
NTPase (NS3) | 984–2081 | 2 | 0 (1) | 18 | 1 (1) | |
p22 (p20, NS4) | 2082–2618 | 3 | 4 (0.01) | 7 | 1 (0.8) | |
VPg (NS5) | 2619–3014 | 1 | 0 (1) | 6 | 0 (1) | |
3CLpro (NS6) | 3015–3560 | 4 | 0 (1) | 2 | 0 (1) | |
RdRp (NS7) | 3561–5090 | 11 | 1 (0.9) | 13 | 0 (1) | |
2 | VP1 | 5074–6690 | 7 | 3 (0.6) | 30 | 9 (0.06) |
|  | S domain | 5074–5736 | 2 | 0 (1) | 9 | 0 (1) |
|  | P1 subdomain | 5737–5895, 6325–6690 | 1 | 0 (1) | 13 | 0 (1) |
|  | P2 subdomain | 5896–6324 | 4 | 3 (0.03) | 8 | 9 (4x10-6) |
3 | VP2 | 6693–7496 | 3 | 4 (0.04) | 10 | 12 (1x10-6) |
| Â | TOTAL | Â | 37 | 14 | 97 | 25 |