TABLE 2.
Posterior distributions of tMRCAs for each subtype data seta
| Subtype/CRF | tMRCA HPD for pol |
tMRCA HPD for env |
||||
|---|---|---|---|---|---|---|
| Mean | Upper value | Lower value | Mean | Upper value | Lower value | |
| CRF01_AE | 1,975.5 | 1,980.5 | 1,970.3 | 1,975.9 | 1,980.6 | 1,970.6 |
| CRF02_AG | 1,976.3 | 1,981.4 | 1,970.5 | 1,975.1 | 1,980.0 | 1,969.0 |
| A1 | 1,954.2 | 1,967.7 | 1,939.7 | 1,954.6 | 1,968.7 | 1,940.3 |
| B | 1,960.3 | 1,968.5 | 1,950.6 | 1,959.2 | 1,966.5 | 1,950.9 |
| B (full genome) | 1,966.1 | 1,972.3 | 1,959.4 | 1,965.3 | 1,970.6 | 1,959.7 |
| C | 1,952.3 | 1,963.4 | 1,940.2 | 1,952.0 | 1,962.3 | 1,939.9 |
| C (full genome) | 1,955.3 | 1,971.8 | 1,933.9 | 1,955.0 | 1,971.5 | 1,934.4 |
| D with prior | 1,946.7 | 1,955.5 | 1,938.0 | 1,944.4 | 1,952.2 | 1,935.4 |
| D without prior | 1,857.0 | 1,932.8 | 1,751.0 | 1,854.1 | 1,931.2 | 1,749.9 |
| G | 1,969.7 | 1,978.3 | 1,959.9 | 1,969.3 | 1,977.3 | 1,959.9 |
a
The tMRCA was estimated using MCMC analysis, using the software BEAST. For all subtypes, the BSP method with a log normal relaxed-clock assumption was used, except for the pol data set of subtype D, where the exponential-growth demographic model was used instead of BSP. HPD, highest posterior density interval.