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, MPHYingbo 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

BACKGROUND

BACKGROUND

• 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?

• The means of inferring evolutionary relationships through molecular sequencing data. The evolutionary history is usually depicted as a branching, treelike diagram

4

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)5

HIV Sequencing/Genotyping

Schematic of HIV-1 particle (in cross-section) Viral genome

Fragment of the pol region

for VARHS genotyping:

1020 nucleotides

ACTCTTTGGCAACGACCCCTTGTCACAATAAAGATAGGGGGGCAACAAAAGGAAGCTCTATTAG…

HIV GENOTYPING RESULT

Guidelines for genotyping

7

• 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

OBJECTIVES

• 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)

• VARHS – 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

METHODS

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

• .

METHODS

• 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)

METHODS

• 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

METHODS

RESULTS

86%

14%

Male Female

Gender

Age at HIV diagnosis

51%

26%12% 10%

0%

10%

20%

30%

40%

50%

60%

<30 30-39 40-49 >49

Average age: 33 years.

Race/Ethnicity

47%

27%

22%

4%

Hispanic/Latino Black/African American White Other

Country of Origin

59%23%

18%

US-born non-US born Unknown

Identified 16 clusters, representing 49 cases. Each cluster comprised of 3-4 cases. Clusters categorized into 4 cluster types. All subtype B.

MSM Cluster- 56%

MSM/HET Cluster- 6%IDU/HET Cluster- 6%

MSM/IDU Cluster- 6%

“MSM” Transmission Channel

• This cluster of 4 represents the “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

100

99

98

0.005

Characteristics of MSM clusters

Race/Ethnicity No. of clusters (%)Cluster with the same race 5 (38%)Cluster with mixed race 8 (62%)

Age at HIV/AIDS diagnosisCluster of <= 25 only 1 (8%)Cluster of mixed age group 5 (38%)Cluster of > 25 only 7 (54%)

Country originCluster of US-born only 6 (46%)Cluster of Foreign-born only 0Cluster of mixed group 7 (54%)

“MSM/IDU” Transmission Channel

• This cluster of 3 represents “MSM/IDU” Transmission Channel.

MSM, 48yrs, White, Unknown origin, K103N

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

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

99100

0.005

“IDU/HET Female” Transmission Channel

• This cluster of 3 represents 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-born99

100

0.005

“MSM/HET” Transmission Channel

• This cluster of 3 represents MSM/HET transmission channel.

Female HET,19, Latino/Hispanic, Mexico-born

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

MSM, 56, Latino/Hispanic, Mexico-born

100

99

0.005

• 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.

DISCUSSION

• 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

CONCLUSIONS

No conflict of interest to disclose.

CONTACT INFORMATION

Kwa Sey PhD, MPH 600 S. Commonwealth Ave. Suite 1920 Los Angeles,CA90005 esey@ph.lacounty.gov

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.

MSM Only Cluster- 75%

MSM/HET Cluster- 6%

IDU/HET Cluster- 3%

MSM/IDU Cluster- 13%

Other/Unknown Cluster- 3%