National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort.

ABSTRACT:

Background

Recent advances in high-throughput molecular epidemiology are transforming the analysis of viral infections.

Methods

Human immunodeficiency virus (HIV)-1 pol sequences from a Northern Californian cohort (NCC) of 4553 antiretroviral-naive individuals sampled between 1998 and 2016 were analyzed together with 140 000 previously published global pol sequences. The HIV-TRAnsmission Cluster Engine (HIV-TRACE) was used to infer a transmission network comprising links between NCC and previously published sequences having a genetic distance ≤1.5%.

Results

Twenty-five percent of NCC sequences were included in 264 clusters linked to a published sequence, and approximately one third of these (8.0% of the total) were linked to 1 or more non-US sequences. T

SUBMITTER: Rhee SY 

PROVIDER: S-EPMC6483754 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature