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Using Phylogenetic Analysis to Identify HIV Transmission Channels among Persons Newly Diagnosed with HIV-1 Infection in Los Angeles County, 2009-2010. Kwa Sey, PhD, MPH Yingbo Ma, MS Nannie Song, MPH . BACKGROUND.

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kwa sey phd mph yingbo ma ms nannie song mph
Using Phylogenetic Analysis to Identify HIV Transmission Channels among Persons Newly Diagnosed with HIV-1 Infection in Los Angeles County, 2009-2010

Kwa Sey, PhD, MPH

Yingbo Ma, MS

Nannie Song, MPH

  • Los Angeles County ranks second in nation only to New York City for highest number of living AIDS cases
  • Between 1982-2010, cumulative total of 75,114 persons with HIV/AIDS reported in LAC
  • Major transmission channels indicated by self-report:
    • male to male sex (79%)
    • heterosexual sex (12%)
    • injection drug use (9%)

*2010 Annual HIV Surveillance Report, January 2011:1-32, HIV Epidemiology Program., LAC-DPH

  • New techniques, such as phylogenetic analysis of HIV sequence data, can provide biological evidence for HIV transmission channels and signal emerging trends
what is phylogenetic analysis
What is Phylogenetic analysis?
  • The means of inferring evolutionary relationships through molecular sequencing data. The evolutionary history is usually depicted as a branching, treelike diagram
what is phylogenetic analysis1
What is Phylogenetic analysis?
  • Phylogenetic relationships used to infer epidemiological links among individuals, such as persons infected with HIV
  • Phylogenetic analysis used to understand patterns of HIV transmission among young black MSM in Mississippi.
  • (CDC, 2011)
hiv sequencing genotyping
HIV Sequencing/Genotyping

Schematic of HIV-1 particle

(in cross-section)

Viral genome



Fragment of the pol region for VARHS genotyping: 1020 nucleotides

guidelines for genotyping
Guidelines for genotyping
  • Genotyping now recommended for all newly diagnosed HIV infected individuals, presenting us with increasingly comprehensive HIV sequence data and opportunity to investigate population level HIV transmission patterns
  • Objective of this analysis to use phylogenetic analyses to characterize HIV transmission channels in Los Angeles County
  • Obtained HIV genomic sequences from VARHS (Variant Atypical and Resistant HIV Surveillance System)
    • extension of the existing national population-based HIV/AIDS case surveillance system
    • coordinated and funded by CDC
  • Since 2006, as part of VARHS, the LAC DHSP HIV Epidemiology has obtained HIV pol region genetic sequences from county residents newly diagnosed with HIV

For inclusion in this analysis, cases had to be:

  • LAC residents
  • Newly diagnosed with HIV
  • Reported to eHARS following a confidential HIV test
  • Antiretroviral naïve
  • Have available genomic sequence (pol region) data from specimen collected within 3 months of diagnosis
  • .
  • Obtained genetic sequencing data for 1,407 (29%) out of 4933 LAC HIV cases diagnosed between 2009 and 2010
  • HIV sequence data merged with demographic and risk behavior data from the Enhanced HIV/AIDS Reporting System (eHARS)
  • Neighbor joining phylogenetic analysis performed on pol sequence spanning protease and reverse transcriptase
  • Nucleotide distances calculated using Kimura's two-parameter method in MEGA5, with 1000 bootstrap replications
  • Transmission clusters defined as sequences that had:
    • common node of bootstrap values greater than 95% and
    • average genetic distance lower than 0.015 nucleotide substitutions per site
age at hiv diagnosis
Age at HIV diagnosis

Average age: 33 years.

MSM Cluster- 56%

MSM/IDU Cluster- 6%

MSM/HET Cluster- 6%

IDU/HET Cluster- 6%

Identified 16 clusters, representing 49 cases.

Each cluster comprised of 3-4 cases.

Clusters categorized into 4 cluster types.

All subtype B.

msm transmission channel
MSM,19yrs, White, USA-born


MSM, 21yrs, White, USA-born


MSM, 25yrs, Latino/Hispanic, USA-born


MSM, 20yrs, Black/African American, USA-born


“MSM” Transmission Channel
  • This cluster of 4 represents the “MSM” Transmission Channel.
msm idu transmission channel
MSM, 48yrs, White, Unknown origin, K103N



MSM, 41yrs, White, USA-born, K103N

Male IDU, 31yrs,Black/African American, USA-born


“MSM/IDU” Transmission Channel
  • This cluster of 3 represents “MSM/IDU” Transmission Channel.
idu het female transmission channel
Male Child, 2, Latino/Hispanic, USA-born

Female IDU,18, Latino/Hispanic, USA-born


Female HET, 39, Latino/Hispanic, USA-born



“IDU/HET Female” Transmission Channel
  • This cluster of 3 represents IDU/HET female transmission channel.
msm het transmission channel
Female HET,19, Latino/Hispanic, Mexico-born


Female HET , 35, Latino/Hispanic, USA-born


MSM, 56, Latino/Hispanic, Mexico-born


“MSM/HET” Transmission Channel
  • This cluster of 3 represents MSM/HET transmission channel.
  • The results provide biological evidence for the major HIV transmission channels that have previously been established by traditional epidemiological data.
  • Small sample size limits the inferences that may be made based on this data.
  • Phylogenetic analysis has potential to serve as additional source of information to validate descriptions of local HIV epidemics inferred from self-reported behavioral data and case studies
contact information

KwaSey PhD, MPH

600 S. Commonwealth Ave. Suite 1920

Los Angeles,CA90005

[email protected]

MSM Only Cluster- 75%

MSM/IDU Cluster- 13%

IDU/HET Cluster- 3%

MSM/HET Cluster- 6%

Other/Unknown Cluster- 3%

85% Boot strap Value Cutoff: 32 clusters, representing 110 cases, were identified. Each of these clusters comprised of 3-6 cases. The clusters were categorized into 5 cluster types. All were subtype B.