TABLE 2.
Evolutionary characteristics of CRF08_BC, CRF07_BC, and subtype C
| HIV-1 strain or subtype and location | Genetic region | Value (HPD) of the evolutionary parameter according to the indicated model:a
|
|||||
|---|---|---|---|---|---|---|---|
| HKY+Γ4 constant size
|
HKY+Γ4 exponential growth
|
HKY+Γ4 logistic growth
|
|||||
| Rate of evolution | tMRCA | Rate of evolution | tMRCA | Rate of evolution | tMRCA | ||
| CRF08_BC | |||||||
| Yunnan and Gansu | gag-pol | 1.8 (1.4, 2.3) | 1990.3 (1988.6, 1991.9) | 1.8 (1.4, 2.3) | 1989.8 (1988.0, 1991.6) | 1.7 (1.3, 2.1) | 1989.3 (1987.3, 1991.0) |
| Liaoning | 1995.6 (1993.4, 1997.5) | 1995.2 (1993.0, 1997.4) | 1995.1 (1992.6, 1997.3) | ||||
| Guangxi | |||||||
| Baise | 1995.5 (1994.3, 1996.5) | 1995.3 (1994.1, 1996.6) | 1995.3 (1993.8, 1996.4) | ||||
| Binyang | |||||||
| Cluster 1 | 1997.1 (1996.3, 1997.9) | 1996.9 (1996.0, 1997.7) | 1996.8 (1995.9, 1997.6) | ||||
| Cluster 2 | 1998.3 (1997.0, 1999.4) | 1998.0 (1996.6, 1999.3) | 1998.0 (1996.6, 1999.3) | ||||
| Cluster 3 | 1998.5 (1997.3, 1999.5) | 1998.4 (1997.1, 1999.5) | 1998.3 (1997.1, 1999.4) | ||||
| Pingxiang | 1999.3 (1998.5, 1999.9) | 1999.2 (1998.3, 1999.9) | 1999.2 (1998.3, 1999.9) | ||||
| CRF07_BC | |||||||
| Yunnan, Xinjiang, and Liaoningb | gag | 4.4 (3.1, 5.7) | 1993.3 (1991.2, 1995.2) | 3.5 (2.1, 4.7) | 1989.4 (1986.2, 1992.2) | 3.9 (2.6, 5.1) | 1992.0 (1989.5, 1994.3) |
| Taiwanc | |||||||
| Tainan (Southern) | env | 4.8 (3.0, 6.6) | 1999.7 (1998.2, 2001.1) | 4.9 (3.0, 6.6) | 1999.7 (1998.2, 2001.0) | 4.2 (2.6, 5.9) | 1999.1 (1997.5, 2000.6) |
| Taipei and Nantou (northern-central) | 2002.1 (2001.3, 2002.9) | 2002.1 (2001.1, 2002.8) | 2001.7 (2000.7, 2002.7) | ||||
| Subtype C | |||||||
| Global | gag-pol | 1.8 (1.4, 2.3) | 1967.6 (1962.5, 1972.0) | 1.8 (1.4, 2.3) | 1966.9 (1962.1, 1971.6) | 1.7 (1.3, 2.1) | 1970.3 (1967.0, 1973.7) |
| India | gag-pol | 1.8 (1.4, 2.3) | 1979.7 (1976.9, 1982.3) | 1.8 (1.4, 2.3) | 1979.5 (1976.3, 1982.6) | 1.7 (1.3, 2.1) | 1977.8 (1974.7, 1980.7) |
| env | 5.6 (3.1, 7.6) | 1976.9 (1972.1, 1981.5) | 5.2 (3.1, 7.0) | 1978.7 (1974.8, 1982.8) | 5.2 (3.3, 7.3) | 1978.2 (1973.9, 1982.1) | |
| China | env | 5.6 (3.1, 7.6) | 1981.2 (1976.7, 1985.9) | 5.2 (3.1, 7.0) | 1982.3 (1978.8, 1985.5) | 5.2 (3.3, 7.3) | 1982.0 (1978.1, 1985.2) |
a
Rates of evolution are expressed as 10−3 nucleotide substitutions per site per year. The 95% highest posterior density (HPD) confidence intervals are given in parentheses.
b
Five patients recruited in Liaoning are reported as having acquired HIV infection outside Liaoning (see Table 1).
c
Constant size and exponential growth analyses based on the hypervariable region-stripped env gene previously described (43).