HIV-1 phylodynamic analysis among people who inject drugs in Pakistan correlates with trends in illicit opioid trade.
Adult
Analgesics, Opioid
/ administration & dosage
Cross-Sectional Studies
Female
HIV Infections
/ epidemiology
HIV Seropositivity
HIV-1
/ isolation & purification
Humans
Male
Opioid-Related Disorders
/ epidemiology
Pakistan
/ epidemiology
Phylogeny
Substance Abuse, Intravenous
/ epidemiology
Young Adult
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
01
06
2019
accepted:
30
07
2020
entrez:
29
8
2020
pubmed:
29
8
2020
medline:
9
10
2020
Statut:
epublish
Résumé
Pakistan is considered by the World Health Organization to currently have a "concentrated" HIV-1 epidemic due to a rapid rise in infections among people who inject drugs (PWID). Prevalence among the country's nearly 105,000 PWID is estimated to be 37.8% but has been shown to be higher in several large urban centers. A lack of public health resources, the common use of professional injectors and unsafe injection practices are believed to have fueled the outbreak. Here we evaluate the molecular characteristics of HIV-1 sequences (n = 290) from PWID in several Pakistani cities to examine transmission dynamics and the association between rates of HIV-1 transmission with regards to regional trends in opioid trafficking. Tip-to-tip (patristic) distance based phylogenetic cluster inferences and BEAST2 Bayesian phylodynamic analyses of time-stamped data were performed on HIV-1 pol sequences generated from dried blood spots collected from 1,453 PWID as part of a cross-sectional survey conducted in Pakistan during 2014/2015. Overall, subtype A1 strains were dominant (75.2%) followed by CRF02_AG (14.1%), recombinants/unassigned (7.2%), CRF35_AD (2.1%), G (1.0%) and C (0.3%). Nearly three quarters of the PWID HIV-1 sequences belonged to one of five distinct phylogenetic clusters. Just below half (44.4%) of individuals in the largest cluster (n = 118) did seek help injecting from professional injectors which was previously identified as a strong correlate of HIV-1 infection. Spikes in estimated HIV-1 effective population sizes coincided with increases in opium poppy cultivation in Afghanistan, Pakistan's western neighbor. Structured coalescent analysis was undertaken in order to investigate the spatial relationship of HIV-1 transmission among the various cities under study. In general terms, our analysis placed the city of Larkana at the center of the PWID HIV-1 epidemic in Pakistan which is consistent with previous epidemiological data.
Identifiants
pubmed: 32857765
doi: 10.1371/journal.pone.0237560
pii: PONE-D-19-15582
pmc: PMC7454939
doi:
Substances chimiques
Analgesics, Opioid
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0237560Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Syst Biol. 2016 Mar;65(2):250-64
pubmed: 26526428
Sex Transm Infect. 2013 Sep;89 Suppl 2:ii18-28
pubmed: 23314301
J Antimicrob Chemother. 2010 Aug;65(8):1562-6
pubmed: 20542904
AIDS. 2011 Jul 17;25(11):1427-30
pubmed: 21516026
Int J STD AIDS. 2004 Mar;15(3):209
pubmed: 15038874
PLoS Comput Biol. 2014 Apr 10;10(4):e1003537
pubmed: 24722319
AIDS. 2010 Jul;24 Suppl 2:S77-84
pubmed: 20610953
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Mol Biol Evol. 2005 May;22(5):1185-92
pubmed: 15703244
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904
BMC Infect Dis. 2010 Jan 12;10:7
pubmed: 20064274
AIDS Res Hum Retroviruses. 1988 Apr;4(2):149-54
pubmed: 3365358
Virus Evol. 2018 Jun 08;4(1):vey016
pubmed: 29942656
Syst Biol. 2018 Sep 1;67(5):901-904
pubmed: 29718447
J Antimicrob Chemother. 2011 Dec;66(12):2823-6
pubmed: 21930572
Bioinformatics. 2014 Nov 15;30(22):3276-8
pubmed: 25095880
Asia Pac J Public Health. 2010 Jul;22(3 Suppl):159S-167S
pubmed: 20566549
Harm Reduct J. 2009 Jun 26;6:13
pubmed: 19558668
J Pak Med Assoc. 2010 Apr;60(4):300-7
pubmed: 20419976
BMC Bioinformatics. 2013 Nov 06;14:317
pubmed: 24191891
Virus Evol. 2015 May 26;1(1):vev003
pubmed: 27774277
J Acquir Immune Defic Syndr. 2009 May 1;51(1):85-90
pubmed: 19289969
Lancet HIV. 2018 Dec;5(12):e678-e679
pubmed: 30527323
Nucleic Acids Res. 2014 Oct;42(18):e144
pubmed: 25120265
Sex Transm Infect. 2013 Sep;89 Suppl 2:ii11-7
pubmed: 23843454
PLoS Comput Biol. 2009 Nov;5(11):e1000581
pubmed: 19956739
PLoS One. 2016 Dec 14;11(12):e0167839
pubmed: 27973597
PLoS One. 2011;6(7):e22449
pubmed: 21799857
J Clin Microbiol. 2012 Jun;50(6):1936-42
pubmed: 22403431
J Mol Evol. 2002 Feb;54(2):156-65
pubmed: 11821909
J Infect Dis. 2015 Mar 15;211(6):926-35
pubmed: 25312037
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Bioinformatics. 2014 Aug 15;30(16):2272-9
pubmed: 24753484
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Mol Biol Evol. 2013 May;30(5):1188-95
pubmed: 23418397
Infect Genet Evol. 2013 Oct;19:337-48
pubmed: 23660484