Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing.
Rapid evolution and high intrahost sequence diversity are hallmarks of human and simian immunodeficiency virus (HIV/SIV) infection. Minor viral variants have important implications for drug resistance, receptor tropism, and immune evasion. Here, we used ultradeep pyrosequencing to sequence complete HIV/SIV genomes, detecting variants present at a frequency as low as 1%. This approach provides a more complete characterization of the viral population than is possible with conventional methods, revealing low-level drug resistance and detecting previously hidden changes in the viral population. While this work applies pyrosequencing to immunodeficiency viruses, this approach could be applied to virtually any viral pathogen.
Bimber
Benjamin N
BN
University of Wisconsin-Madison, Madison, WI 53711, USA.
Dudley
Dawn M
DM
Lauck
Michael
M
Becker
Ericka A
EA
Chin
Emily N
EN
Lank
Simon M
SM
Grunenwald
Haiying L
HL
Caruccio
Nicholas C
NC
Maffitt
Mark
M
Wilson
Nancy A
NA
Reed
Jason S
JS
Sosman
James M
JM
Tarosso
Leandro F
LF
Sanabani
Sabri
S
Kallas
Esper G
EG
Hughes
Austin L
AL
O'Connor
David H
DH
D000595:Amino Acid Sequence; D000818:Animals; D014644:Genetic Variation; D016679:Genome, Viral; D006678:HIV / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D015658:HIV Infections / Q000276:immunology / Q000821:virology; D006801:Humans; D008253:Macaca mulatta; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D016097:Simian Acquired Immunodeficiency Syndrome / Q000276:immunology / Q000821:virology; D015302:Simian Immunodeficiency Virus / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D013045:Species Specificity; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
D014764:Viral Proteins