Identifying Clusters of Recent and Rapid HIV Transmission Through Analysis of Molecular Surveillance Data

Journal of Acquired Immune Deficiency Syndromes : JAIDS
Alexandra M OsterAngela L Hernandez

Abstract

Detecting recent and rapid spread of HIV can help prioritize prevention and early treatment for those at highest risk of transmission. HIV genetic sequence data can identify transmission clusters, but previous approaches have not distinguished clusters of recent, rapid transmission. We assessed an analytic approach to identify such clusters in the United States. We analyzed 156,553 partial HIV-1 polymerase sequences reported to the National HIV Surveillance System and inferred transmission clusters using 2 genetic distance thresholds (0.5% and 1.5%) and 2 periods for diagnoses (all years and 2013-2015, ie, recent diagnoses). For rapidly growing clusters (with ≥5 diagnoses during 2015), molecular clock phylogenetic analysis estimated the time to most recent common ancestor for all divergence events within the cluster. Cluster transmission rates were estimated using these phylogenies. A distance threshold of 1.5% identified 103 rapidly growing clusters using all diagnoses and 73 using recent diagnoses; at 0.5%, 15 clusters were identified using all diagnoses and 13 using recent diagnoses. Molecular clock analysis estimated that the 13 clusters identified at 0.5% using recent diagnoses had been diversifying for a median of 4.7 yea...Continue Reading

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Citations

Mar 19, 2019·Current Opinion in HIV and AIDS·Joel O WertheimArt F Y Poon
Apr 28, 2019·The Journal of Infectious Diseases·Anne Marie France, Alexandra M Oster
Oct 22, 2019·AIDS·Jessica M FogelSusan H Eshleman
Mar 13, 2020·MMWR. Morbidity and Mortality Weekly Report·Bridget J AndersonAlexandra M Oster
Feb 6, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Adiba HassanJoel O Wertheim
Jun 23, 2020·Briefings in Bioinformatics·Sergey KnyazevAlexander Zelikovsky
Dec 28, 2019·The New England Journal of Medicine·Gregory L ArmstrongMarta Gwinn
Oct 6, 2020·The American Journal of Bioethics : AJOB·Meg Watson, Patricia Sweeney
Apr 20, 2019·Frontiers in Microbiology·Elena DelgadoUNKNOWN Spanish Group for the Study of New HIV Diagnoses
Aug 12, 2020·Public Health Reports·Donna Hubbard McCreePaul J Weidle
Apr 20, 2019·Emerging Infectious Diseases·Arthur G FitzmauriceAlexandra M Oster
Aug 3, 2020·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Amy R BoardAnne Marie France
Jan 22, 2021·Journal of the International AIDS Society·Francesca Di GiallonardoUNKNOWN NSW HIV Prevention Partnership Project
Oct 31, 2020·Scientific Reports·Vlad NovitskyRami Kantor
Sep 6, 2020·Sexually Transmitted Diseases·Laura A S QuilterKyle Bernstein
Jan 5, 2021·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Niema MoshiriSiavash Mirarab
Feb 16, 2021·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Susan J LittleDavey M Smith
Apr 3, 2021·Translational Research : the Journal of Laboratory and Clinical Medicine·Charles MarksAnnick Bórquez
Apr 25, 2021·Mathematical Biosciences and Engineering : MBE·Sonza SinghChaitra Gopalappa
May 16, 2021·Health Care Management Science·Matthew EdenChaitra Gopalappa

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