TY - JOUR
T1 - HIV type 1 in a rural coastal town in Kenya shows multiple introductions with many subtypes and much recombination
AU - Hué, Stéphane
AU - Hassan, Amin S.
AU - Nabwera, Helen
AU - Sanders, Eduard J.
AU - Pillay, Deenan
AU - Berkley, James A.
AU - Cane, Patricia A.
PY - 2012/2/1
Y1 - 2012/2/1
N2 - The extent of HIV-1 diversity was examined among patients attending a rural district hospital in a coastal area of Kenya. The pol gene was sequenced in samples from 153 patients. Subtypes were designated using the REGA, SCUEAL, and jpHMM programs. The most common subtype was A1, followed by C and D; A2 and G were also detected. However, a large proportion of the samples was found to be recombinants, which clustered within the pure subtype branches. Phylogeographic analysis of Kilifi sequences compared with those from other regions of Africa showed that while many sequences were closely related to sequences from Kenya, others were most closely related to known sequences from other parts of Africa, including West Africa. Overall, these data indicate that there have been multiple introductions of HIV-1 into this small rural town and surroundings with ongoing diversity being generated by recombination.
AB - The extent of HIV-1 diversity was examined among patients attending a rural district hospital in a coastal area of Kenya. The pol gene was sequenced in samples from 153 patients. Subtypes were designated using the REGA, SCUEAL, and jpHMM programs. The most common subtype was A1, followed by C and D; A2 and G were also detected. However, a large proportion of the samples was found to be recombinants, which clustered within the pure subtype branches. Phylogeographic analysis of Kilifi sequences compared with those from other regions of Africa showed that while many sequences were closely related to sequences from Kenya, others were most closely related to known sequences from other parts of Africa, including West Africa. Overall, these data indicate that there have been multiple introductions of HIV-1 into this small rural town and surroundings with ongoing diversity being generated by recombination.
UR - http://www.scopus.com/inward/record.url?scp=84858048436&partnerID=8YFLogxK
U2 - 10.1089/aid.2011.0048
DO - 10.1089/aid.2011.0048
M3 - Article
C2 - 21770741
AN - SCOPUS:84858048436
SN - 0889-2229
VL - 28
SP - 220
EP - 224
JO - AIDS Research and Human Retroviruses
JF - AIDS Research and Human Retroviruses
IS - 2
ER -
