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

Carlisle, Louisa A; Turk, Teja; Kusejko, Katharina; Metzner, Karin J; Leemann, Christine; Schenkel, Corinne; Bachmann, Nadine; Posada, Susana; Beerenwinkel, Niko; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Braun, Dominique L; Rauch, Andri; Calmy, Alexandra; Cavassini, Matthias; Battegay, Manuel; Vernazza, Pietro; Bernasconi, Enos; ... (2019). Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection. The journal of infectious diseases, 220(2), pp. 254-265. Oxford University Press 10.1093/infdis/jiz094

[img] Text
J Infect Dis 19.pdf - Accepted Version
Restricted to registered users only until 5 April 2020.
Available under License Publisher holds Copyright.

Download (1MB) | Request a copy
[img] Text
jiz094.pdf - Published Version
Restricted to registered users only
Available under License Publisher holds Copyright.

Download (1MB) | Request a copy

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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Infectiology

UniBE Contributor:

Rauch, Andri

Subjects:

600 Technology > 610 Medicine & health

ISSN:

1537-6613

Publisher:

Oxford University Press

Language:

English

Submitter:

Annelies Luginbühl

Date Deposited:

23 May 2019 17:08

Last Modified:

23 Oct 2019 10:35

Publisher DOI:

10.1093/infdis/jiz094

PubMed ID:

30835266

Uncontrolled Keywords:

HIV-1 diversity infection recency next-generation sequencing time since infection

BORIS DOI:

10.7892/boris.127861

URI:

https://boris.unibe.ch/id/eprint/127861

Actions (login required)

Edit item Edit item
Provide Feedback