Evaluation of sequence ambiguities of the HIV-1 pol gene as a method to identify recent HIV-1 infection in transmitted drug resistance surveys

• Published in: Infection, genetics and evolution Vol. 18; pp. 125 - 131
• Main Authors: Andersson, Emmi, Shao, Wei, Bontell, Irene, Cham, Fatim, Cuong, Do Duy, Wondwossen, Amogne, Morris, Lynn, Hunt, Gillian, Sönnerborg, Anders, Bertagnolio, Silvia, Maldarelli, Frank, Jordan, Michael R.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2013
• Subjects: Ambiguity; Bioinformatics; Chronic Disease; Databases, Genetic; Drug Resistance, Viral; Female; Genes, pol; HIV; HIV Infections - classification; HIV Infections - epidemiology; HIV Infections - transmission; HIV Infections - virology; HIV-1 - genetics; Humans; Incidence; Male; Medicin och hälsovetenskap; Resistance; Sequence Alignment; Sequence Analysis, RNA; Viral diversity; Resistance; Viral diversity; HIV; Bioinformatics; Ambiguity; Incidence

•We analyze 691 recent and chronic HIV pol sequences for proportion of mixed bases.•Significant difference in proportion is seen between recent and chronic infection.•A cutoff of <0.47% mixed bases to identify recent (<1year) infection is established.•We apply it to 36 TDR surveys and 71% of i...