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) |
| TOTAL | 37 | 14 | 97 | 25 | ||
*P-values were calculated using binomial distribution and indicate the probability of observing the corresponding number of non-synonymous single nucleotide variants in the specified region after controlling for gene/domain size