TABLE 3.
Estimated days since infection and 95% confidence/credible intervals obtained by PF and BEAST, respectively, for animals infected with multiple variantsa
| Animal and setting | Estimated no. of days (CI) since infection |
|||
|---|---|---|---|---|
| Site removed |
Site not removed |
|||
| Poisson fitter | BEAST | Poisson fitter | BEAST | |
| RM131, no APOBEC, day 14 | 14 (8, 20) | 23 (7, 44) | 17 (13, 21) | 50 (19, 90) |
| RM131, day 21 | 28 (19, 38) | 32 (16, 53) | 25 (20, 30) | 54 (24, 93) |
| RM138, no APOBEC, day 14 | 22 (15, 28) | 27 (12, 47) | 18 (15, 21) | 54 (20, 92) |
| RM6454, day 28 | 32 (19, 45) | 39 (19, 68) | 18 (15, 21) | 55 (22, 96) |
| RM944, no APOBEC, day 28 | 32 (24, 39) | 34 (15, 59) | 32 (28, 36) | 55 (24, 94) |
| RM43335, day 28 | 17 (12, 21) | 21 (8, 36) | 16 (14, 19) | 38 (14, 70) |
| RM6072, no APOBEC, day 28 | 34 (21, 47) | 40 (18, 67) | 39 (22, 56) | 52 (22, 85) |
| RM6446, no APOBEC, day 28 | 27 (19, 35) | 32 (15, 54) | 30 (21, 38) | 35 (17, 56) |
a
The data in columns 2 and 3 represent results obtained after removing the site(s) at which the distinct inoculum variants differed, whereas the data in columns 4 and 5 represent the results from the original samples, as described in the main text, with the codon at 375 (or, in two cases, at 133 and 138) left in.