The Number and Complexity of Pure and Recombinant HIV-1 Strains Observed within Incident Infections during the HIV and Malaria Cohort Study Conducted in Kericho, Kenya, from 2003 to 2006.
Characterization of HIV-1 subtype diversity in regions where vaccine trials are conducted is critical for vaccine development and testing. This study describes the molecular epidemiology of HIV-1 within a tea-plantation community cohort in Kericho, Kenya. Sixty-three incident infections were ascertained in the HIV and Malaria Cohort Study conducted in Kericho from 2003 to 2006. HIV-1 strains from 58 of those individuals were full genome characterized and compared to two previous Kenyan studies describing 41 prevalent infections from a blood bank survey (1999-2000) and 21 infections from a higher-risk cohort containing a mix of incident and prevalent infections (2006). Among the 58 strains from the community cohort, 43.1% were pure subtypes (36.2% A1, 5.2% C, and 1.7% G) and 56.9% were inter-subtype recombinants (29.3% A1D, 8.6% A1CD, 6.9% A1A2D, 5.2% A1C, 3.4% A1A2CD, and 3.4% A2D). This diversity and the resulting genetic distance between the observed strains will need to be addressed when vaccine immunogens are chosen. In consideration of current vaccine development efforts, the strains from these three studies were compared to five candidate vaccines (each of which are viral vectored, carrying inserts corresponding to parts of gag, pol, and envelope), which have been developed for possible use in sub-Saharan Africa. The sequence comparison between the observed strains and the candidate vaccines indicates that in the presence of diverse recombinants, a bivalent vaccine is more likely to provide T-cell epitope coverage than monovalent vaccines even when the inserts of the bivalent vaccine are not subtype-matched to the local epidemic.
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Erik
E
Billings
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Eric
E
Sanders-Buell
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Meera
M
Bose
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Andrea
A
Bradfield
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Esther
E
Lei
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Gustavo H
GH
Kijak
United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America.
Miguel A
MA
Arroyo
The Kenya Medical Research Institute/Walter Reed Project Clinical Research Center, Kericho, Kenya.
Rukia M
RM
Kibaya
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Paul T
PT
Scott
The Kenya Medical Research Institute, Kericho, Kenya; The Kenya Medical Research Institute, Nairobi, Kenya.
Monique K
MK
Wasunna
The Kenya Medical Research Institute/Walter Reed Project HIV Program, Kericho, Kenya.
Frederick K
FK
Sawe
United States Army Medical Research Unit-Kenya/Walter Reed Project HIV Program, Kericho, Kenya.
Douglas N
DN
Shaffer
United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America.
Deborah L
DL
Birx
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Francine E
FE
McCutchan
United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America.
Nelson L
NL
Michael
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Merlin L
ML
Robb
International Vaccine Institute, Seoul, Republic of Korea.
Jerome H
JH
Kim
United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America.
Sodsai
S
Tovanabutra
D016915:AIDS Vaccines / Q000276:immunology*; D001483:Base Sequence; D015331:Cohort Studies; D004279:DNA, Viral / Q000235:genetics*; D018984:Epitopes, T-Lymphocyte / Q000276:immunology; D015658:HIV Infections / Q000150:complications / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000276:immunology; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D008288:Malaria / Q000150:complications / Q000453:epidemiology / Q000469:parasitology; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D054299:env Gene Products, Human Immunodeficiency Virus / Q000276:immunology; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000276:immunology; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000276:immunology
D016915:AIDS Vaccines; D004279:DNA, Viral; D018984:Epitopes, T-Lymphocyte; D054299:env Gene Products, Human Immunodeficiency Virus; D054301:gag Gene Products, Human Immunodeficiency Virus; D054302:pol Gene Products, Human Immunodeficiency Virus