Longitudinal phylogenetic surveillance identifies distinct patterns of cluster dynamics

Journal of Acquired Immune Deficiency Syndromes : JAIDS
Manon Ragonnet-CroninJames I Brooks

Abstract

Through the application of simple, accessible, molecular epidemiology tools, we aimed to resolve the phylogenetic relationships that best predicted patterns of cluster growth using longitudinal population level drug resistance genotype data. Analysis was performed on 971 specimens from drug naïve, first time HIV positive subjects collected in British Columbia between 2002 and 2005. A 1240bp fragment of the pol gene was amplified and sequenced with relationships among subtype B sequences inferred using Neighbour-Joining analysis. Apparent clusters of infections having both a mean within group distance <0.031 and bootstrap value >80% were systematically identified. The entire 2002-2005 dataset was then re-analyze to evaluate the relationship of subsequent infections to those identified in 2002. BED testing was used to identify recent infections (<156 days). Among the 2002 infections, 136 of 300 sequences sorted into 52 clusters ranging in size from 2 to 9 members. Aboriginal ethnicity and intravenous drug use were correlated, and both were linked to cluster membership in 2002. Although cluster growth between 2002 and 2005 was correlated with the size of the original cluster, more related infections were found in clusters seeded f...Continue Reading

References

Oct 1, 1996·Proceedings of the National Academy of Sciences of the United States of America·T LeitnerJ Albert
Jan 7, 1997·Proceedings of the National Academy of Sciences of the United States of America·M E WoolhouseR M Anderson
Jul 11, 2001·AIDS Patient Care and STDs·D W Fitzgerald, T B Simon
May 4, 2004·The Journal of Infectious Diseases·Christopher D PilcherUNKNOWN Duke-UNC-Emory Acute HIV Consortium
Jul 21, 2004·Briefings in Bioinformatics·Sudhir KumarMasatoshi Nei
Nov 18, 2005·Nature·Alison P Galvani, Robert M May
Mar 3, 2007·The Journal of Infectious Diseases·Bluma G BrennerUNKNOWN Quebec Primary HIV Infection Study Group
Sep 8, 2007·BMJ : British Medical Journal·Deenan PillayAndrew J Leigh Brown
Dec 8, 2007·AIDS and Behavior·Steven D Pinkerton
Dec 20, 2007·AIDS·Sabine YerlyUNKNOWN Swiss HIV Cohort Study
Dec 27, 2007·The Canadian Journal of Infectious Diseases = Journal Canadien Des Maladies Infectieuses·G C JayaramanD Sutherland
Mar 21, 2008·PLoS Medicine·Fraser LewisAndrew J Leigh Brown
Mar 21, 2008·PLoS Medicine·Christopher D PilcherSatish K Pillai
Jun 14, 2008·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Martin S HirschDouglas D Richman
Aug 1, 2008·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Matthew KayeChris Birch
Oct 2, 2008·HIV Medicine·B G GazzardUNKNOWN BHIVA Treatment Guidelines Writing Group
Sep 26, 2009·PLoS Pathogens·Gareth J HughesUNKNOWN UK HIV Drug Resistance Collaboration
Nov 28, 2009·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Mt CuevasUNKNOWN Study group of HIV-1 newly diagnosed patients in Galicia, Spain

❮ Previous
Next ❯

Citations

May 26, 2011·Nature Communications·Mattia C F ProsperiUNKNOWN ARCA collaborative group
Jun 16, 2012·AIDS Research and Human Retroviruses·Michael S MacVeighThomas P Young
Aug 27, 2013·AIDS Research and Human Retroviruses·Richard A HeipertzSodsai Tovanabutra
Jun 29, 2012·AIDS·Ann M DennisJoseph J Eron
May 18, 2012·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Delivette CastorMartin Markowitz
Jun 14, 2012·PloS One·Manon Ragonnet-CroninJames Brooks
May 14, 2014·Annual Review of Genomics and Human Genetics·Shiven B ChabriaMichael J Kozal
Dec 26, 2015·The Journal of Infectious Diseases·Manon Ragonnet-CroninUNKNOWN UK HIV Drug Resistance Database
Jun 15, 2011·Antiviral Research·Federico GarcíaUNKNOWN Cohort of the Spanish AIDS Research Network (CoRIS)
Aug 11, 2015·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Philip A ChanRami Kantor
Nov 7, 2013·BMC Bioinformatics·Manon Ragonnet-CroninUNKNOWN UK HIV Drug Resistance Database
Jul 12, 2016·African Journal of AIDS Research : AJAR·Usangiphile E ButheleziAyesha Bm Kharsany
Jun 4, 2016·PloS One·Dennis Maletich JunqueiraSabrina Esteves de Matos Almeida
May 8, 2014·Expert Review of Anti-infective Therapy·Juan AmbrosioniJose M Miro
Aug 31, 2017·Virus Evolution·Bethany L DearloveSimon D W Frost
Nov 14, 2018·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Rachael M BillockAnn M Dennis
Jul 1, 2014·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Ann M DennisMyron S Cohen
May 4, 2012·AIDS·Ronald J LubelchekDavid E Barker
Oct 19, 2012·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Anne M AudelinJan Gerstoft
Mar 30, 2017·PLoS Computational Biology·David A RasmussenTanja Stadler
Nov 16, 2013·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Manon Ragonnet-CroninJames I Brooks
Feb 23, 2017·Retrovirology·Antoine ChaillonUNKNOWN on behalf the ANRS PRIMO Cohort Study
Aug 11, 2011·Journal of the International AIDS Society·Malcolm SteinbergMichael L Rekart
Aug 11, 2020·AIDS·Rebecca RoseOliver Laeyendecker
Jun 3, 2021·The Journal of Infectious Diseases·Manon Ragonnet-CroninUNKNOWN with the PANGEA Consortium

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antimicrobial Resistance

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.