Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection

Publication

Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection

Journal Paper/Review - Mar 4, 2019

Carlisle Louisa A, Braun Dominique L, Rauch Andri, Calmy Alexandra, Cavassini Matthias, Battegay Manuel, Vernazza Pietro, Bernasconi Enos, Günthard Huldrych F, Kouyos Roger D, Perreau Matthieu, Klimkait Thomas, Yerly Sabine, Turk Teja, Kusejko Katharina, Metzner Karin J, Leemann Christine, Schenkel Corinne, Bachmann Nadine, Posada Susana, Beerenwinkel Niko, Böni Jürg, Swiss HIV Cohort Study

Citation

Carlisle L, Braun D, Rauch A, Calmy A, Cavassini M, Battegay M, Vernazza P, Bernasconi E, Günthard H, Kouyos R, Perreau M, Klimkait T, Yerly S, Turk T, Kusejko K, Metzner K, Leemann C, Schenkel C, Bachmann N, Posada S, Beerenwinkel N, Böni J, Swiss HIV Cohort Study. Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection. J Infect Dis 2019

Type

Journal Paper/Review (English)

Journal

J Infect Dis 2019

Publication Date

Mar 4, 2019

Issn Electronic

1537-6613

Brief description/objective

BACKGROUND
HIV-1 genetic diversity increases over the course of infection, and can be used to infer time since infection (TSI) and consequently also infection recency, crucial quantities for HIV-1 surveillance and the understanding of viral pathogenesis.

METHODS
We considered 313 HIV-infected individuals for whom reliable estimates of infection dates and next-generation sequencing (NGS)-derived nucleotide frequency data were available. Fraction of ambiguous nucleotides (FAN) obtained by population sequencing were available for 207 samples. We assessed whether average pairwise diversity (APD) calculated using NGS sequences provided a more exact prediction of TSI and classification of infection recency (<1 year post-infection) compared to FAN.

RESULTS
NGS-derived APD classifies an infection as recent with a sensitivity of 88% and specificity of 85%. When considering only the 207 samples for which FAN were available, NGS-derived APD exhibited a higher sensitivity (90% vs 78%) and specificity (95% vs 67%) than FAN. Additionally, APD can estimate TSI with a mean absolute error of 0.84 years, compared to 1.03 years for FAN.